Showing papers in "Molecular Breeding in 2010"
TL;DR: A novel breeding strategy is proposed: disabling plant disease susceptibility genes (S-genes) to achieve durable and broad-spectrum resistance by looking from a different point of view into host and nonhost resistance.
Abstract: Recent studies on plant immunity have suggested that a pathogen should suppress induced plant defense in order to infect a plant species, which otherwise would have been a nonhost to the pathogen. For this purpose, pathogens exploit effector molecules to interfere with different layers of plant defense responses. In this review, we summarize the latest findings on plant factors that are activated by pathogen effectors to suppress plant immunity. By looking from a different point of view into host and nonhost resistance, we propose a novel breeding strategy: disabling plant disease susceptibility genes (S-genes) to achieve durable and broad-spectrum resistance.
296 citations
TL;DR: Marker-trait associations are now known for a number of simple, but difficult-to-score traits, so that MAS has been found useful for improvement of several of these important economic traits.
Abstract: Wheat production and productivity in the past witnessed a remarkable growth. However, this growth rate could not be sustained during the last decade, causing concern among world wheat community. Marker-assisted selection (MAS), which is being practiced for improvement of a variety of traits in wheat around the world, may at least partly help in providing the desired solution. Marker-trait associations are now known for a number of simple, but difficult-to-score traits, so that MAS has been found useful for improvement of several of these important economic traits. Breeding strategies including marker-assisted backcrossing, forward breeding, MAS involving doubled haploid technology and F2 enrichment have been successfully utilized for this purpose. However, for improvement of complex polygenic traits, newer technologies based on high throughput genotyping associated with new marker systems (e.g., DArT and SNP), and new selection strategies such as AB-QTL, mapping-as-you-go, marker-assisted recurrent selection and genome-wide selection will have to be tried in future. The progress made in all these aspects of marker-assisted wheat breeding, and the limitations and future prospects of this emerging technology have been reviewed in this article.
246 citations
TL;DR: Most SNPs used in this GoldenGate assay appear to be equally useful for diversity analysis, marker-trait association studies, and marker-aided breeding.
Abstract: Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the genomes of most plant species. They have become an ideal marker system for genetic research in many crops. Several high throughput platforms have been developed that allow rapid and simultaneous geno- typing of up to a million SNP markers. In this study, a custom GoldenGate assay containing 1,536 SNPs was developed based on public SNP information for maize and used to genotype two recombinant inbred line (RIL) populations (Zong3 x 87-1, and B73 x By804) and a panel of 154 diverse inbred lines. Over 90% of the SNPs were successfully scored in the diversity panel and the two RIL populations, with a genotyping error rate of less than 2%. A total of 975 SNP markers detected polymorphism in at least one of the two mapping populations, with a polymorphic rate of 38.5% in Zong3 x 87-1 and 52.6% in B73 x By804. The polymorphic SNPs in B73 x By804 have been integrated with previously mapped simple sequence repeat markers to construct a high-density linkage map containing 662 markers with a total length of 1,673.7 cM and an average of 2.53 cM between two markers. The minor allelic frequency (MAF) was distributed evenly across 10 continued classes from 0.05 to 0.5, and about 16% of the SNP markers had a MAF below 10% in the diversity panel. Polymorphism rates for individual SNP mark- ers in pair-wise comparisons of genotypes tested ranged from 0.3 to 63.8% with an average of 36.3%. Most SNPs used in this GoldenGate assay appear to be equally useful for diversity analysis, marker-trait association studies, and marker-aided breeding.
241 citations
TL;DR: Efforts on gene expression profiling, deep transcriptome sequencing, high throughput metabolomics and phenotyping of contrasting arsenic accumulating lines need to be increased to develop strategies for design of safer rice varieties.
Abstract: Arsenic is commonly present in subsoil and is a carcinogen in humans. Rice takes up arsenic and it accumulates in different plant parts, including grains, at levels several-fold higher than the soil. In high arsenic regions, rice can contribute substantially to arsenic intake by the human population. Arsenic in rice grains is present in the carcinogenic inorganic or the relatively safer organic (methylated) form. A wide variation is noticed in different rice genotypes with respect to the proportion of arsenic in these forms in grains. Mechanisms involved in arsenic uptake, efflux from roots, loading into xylem, transport, partitioning, arsenate reduction, arsenic sequestration in vacuoles, volatilization from leaves, accumulation in grains etc. are poorly understood. Selection of cultivars accumulating low inorganic arsenic is an important trait to be used by breeders to develop rice varieties safer for cultivation in arsenic-contaminated regions. Systematic efforts have not been made to screen rice genotypes for mining the genes involved in arsenic uptake, transport and accumulation in grains. Identification of rice germplasm with varying arsenic uptake and partitioning, and development of mapping populations with contrasting grain arsenic, are required for association studies and QTL mapping for accelerating rice improvement. Efforts on gene expression profiling, deep transcriptome sequencing, high throughput metabolomics and phenotyping of contrasting arsenic accumulating lines need to be increased to develop strategies for design of safer rice varieties. Network research projects need to be developed along these approaches to accelerate the development of crop varieties safer for farming in arsenic-contaminated environments.
206 citations
TL;DR: To model senescence and identify quantitative trait loci for the trait, a population of recombinant inbred lines from a cross between winter wheat cultivars, ‘Ventnor’ and ‘Karl 92’ was evaluated for heat tolerance under optimum temperature and continuous heat stress from 10 days after anthesis (DAA) until maturity.
Abstract: Senescence is a genetically programmed and environmentally influenced process resulting in the destruction of chlorophyll and remobilization of nutrients to younger or reproductive parts of plants. Delayed senescence, or stay-green, contributes to a long grain-filling period and stable yield under stress. To model senescence and identify quantitative trait loci (QTL) for the trait, a population of recombinant inbred lines (RIL) from a cross between winter wheat cultivars, ‘Ventnor’ and ‘Karl 92’ was evaluated for heat tolerance under optimum temperature of 20/15°C (day/night) and continuous heat stress of 30/25°C from 10 days after anthesis (DAA) until maturity. Ventnor is a heat-tolerant cultivar and Karl 92 is a relatively heat-susceptible cultivar. Green leaf area was measured and used to model percent greenness retained over the reproductive period. Chlorophyll content and chlorophyll fluorescence were recorded on flag leaves. Senescence was converted to a quantitative trait using the model. Based on the modeled parameters, the RILs were categorized into three groups. When senescence-related traits were evaluated, nine QTL for heat tolerance were found on chromosome 2A, two each on chromosomes 6A and 6B and one each on chromosome 3A, 3B, and 7A. Both parents contributed favorable alleles for most of the senescence-related traits. Microsatellite markers Xgwm356 and Xgwm5 prominently linked to the senescence-related traits may be useful in marker-assisted breeding. These and the linked AFLP (amplified fragment length polymorphism) markers XCGT.TGCG-349, XCGT.GTG-343, and XCGT.CTCG-406, if converted to STS (sequence tagged sites), can be used for further molecular dissection of the QTL for post-anthesis heat tolerance.
180 citations
TL;DR: There is very high genetic variation among varieties at this locus, which can serve as a starting point for allele mining of sheath blight resistance in rice line Tetep, which is a well documented source of durable and broad spectrum resistance to rice blast as well as quantitative resistance to she Heath blight.
Abstract: Sheath blight caused by Rhizoctonia solani Kuhn is one of the important diseases of rice, resulting in heavy yield loss in rice every year. No rice line resistant to sheath blight has been identified till date. However, in some rice lines a high degree of resistance to R. solani has been observed. An indica rice line, Tetep, is a well documented source of durable and broad spectrum resistance to rice blast as well as quantitative resistance to sheath blight. The present study identified genetic loci for quantitative resistance to sheath blight in rice line Tetep. A mapping population consisting of 127 recombinant inbred lines derived from a cross between rice cultivars HP2216 (susceptible) and Tetep (resistant to sheath blight) was evaluated for sheath blight resistance and other agronomic traits for 4 years across three locations. Based on sheath blight phenotypes and genetic map with 126 evenly distributed molecular markers, a quantitative trait loci (QTLs) contributing to sheath blight resistance was identified on long arm of chromosome 11. Two QTL mapping approaches i.e., single marker analysis and composite interval mapping in multi environments were used to identify QTLs for sheath blight resistance and agronomical traits. The QTL qSBR11-1 for sheath blight resistance was identified between the marker interval RM1233 (26.45 Mb) to sbq33 (28.35 Mb) on chromosome 11. This region was further narrowed down to marker interval K39516 to sbq33 (~0.85 Mb) and a total of 154 genes were predicted including 11 tandem repeats of chitinase genes which may be responsible for sheath blight resistance in rice line Tetep. A set of 96 varieties and a F2 population were used for validation of markers linked to the QTL region. The results indicate that there is very high genetic variation among varieties at this locus, which can serve as a starting point for allele mining of sheath blight resistance.
150 citations
TL;DR: This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor.
Abstract: Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of barley. The disease has been controlled for over 40 years through the deployment of cultivars with durable resistance derived from the line NDB112. Pathotypes of C. sativus with virulence for the NDB112 resistance have been detected in Canada; thus, many commercial cultivars are vulnerable to spot blotch epidemics. To increase the diversity of spot blotch resistance in cultivated barley, we evaluated 318 diverse wild barley accessions comprising the Wild Barley Diversity Collection (WBDC) for reaction to C. sativus at the seedling stage and utilized an association mapping (AM) approach to identify and map resistance loci. A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses. The WBDC was genotyped with 558 Diversity Array Technology (DArT®) and 2,878 single nucleotide polymorphism (SNP) markers and subjected to structure analysis before running the AM procedure. Thirteen QTL for spot blotch resistance were identified with DArT and SNP markers. These QTL were found on chromosomes 1H, 2H, 3H, 5H, and 7H and explained from 2.3 to 3.9% of the phenotypic variance. Nearly half of the identified QTL mapped to chromosome bins where spot blotch resistance loci were previously reported, offering some validation for the AM approach. The other QTL mapped to unique genomic regions and may represent new spot blotch resistance loci. This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor.
146 citations
International Crops Research Institute for the Semi-Arid Tropics1, University of California, Davis2, Indian Institute of Pulses Research3, National Center for Genome Resources4, University of Agricultural Sciences, Dharwad5, Banaras Hindu University6, Tuskegee University7, J. Craig Venter Institute8, Watson School of Biological Sciences9, Purdue University10
TL;DR: The collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeon pea genetics and breeding.
Abstract: Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an ‘orphan crop legume’. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation’s Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an ‘orphan legume crop’ to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.
145 citations
TL;DR: The performance of the BB-resistant version of PusaRH10 produced by intercrossing the improved parental lines was on a par with or superior to the original Pusa RH10.
Abstract: Pusa RH10, the widely cultivated superfine grain aromatic rice hybrid, and its parental lines Pusa6B and PRR78 are susceptible to bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae. Pusa1460, a Basmati rice variety, was utilized as the donor for introgressing BB resistance genes xa13 and Xa21 into Pusa6B and PRR78 using a marker-assisted backcross breeding program. The markers RG136 and pTA248 linked to BB resistance genes xa13 and Xa21, respectively, were used for foreground selection. Seventy-four STMS markers polymorphic between Pusa6B and Pusa1460, and 54 STMS markers polymorphic between PRR78 and Pusa1460, were utilized for background selection to recover the recurrent parent genome ranging from 85.14 to 97.30% and 87.04 to 92.81% in the 10 best BC2F5 families of Pusa6B and PRR78, respectively. RM6100, an STMS marker linked to fertility restorer gene (Rf), was used for marker-assisted selection of Rf gene in an improved version of PRR78. The extent of donor segments in the improved version of Pusa6B was estimated to be <0.97 and <2.15 Mb in the genomic regions flanking xa13 and Xa21, respectively, whereas in improved PRR78, it was estimated to be <2.07 and <3.45 Mb in the corresponding genomic regions. Improved lines of Pusa6B and PRR78 showed yield advantages of up to 8.24 and 5.23%, respectively. The performance of the BB-resistant version of Pusa RH10 produced by intercrossing the improved parental lines was on a par with or superior to the original Pusa RH10.
144 citations
TL;DR: An increasing number of large-scale genetic variant discovery initiatives are being undertaken in conjunction with next-generation sequencing platforms, allowing for drastically quicker and cheaper variant discovery, and leading towards a far more comprehensive view of the genome or transcriptome.
Abstract: Genome-wide variant detection within a species is the primary initial step towards linking genotypic variation and phenotypes The conversion of these genetic variants (the most prevalent of these being single-nucleotide polymorphisms or SNPs) into genetic markers is particularly important in agronomically valuable crop species to allow for cost-effective marker-assisted selection strategies, whole-genome fingerprinting, association studies, map-based gene cloning and population-based analyses Towards these goals, an increasing number of large-scale genetic variant discovery initiatives are being undertaken in conjunction with next-generation sequencing platforms, allowing for drastically quicker and cheaper variant discovery, and leading towards a far more comprehensive view of the genome or transcriptome This review will summarize the current status of these initiatives and will discuss the expanding role of next-generation sequencing technologies in facilitating crop improvement
137 citations
TL;DR: It is concluded that innovative models for resource-pooling and intellectual-property-respecting partnerships will be required for enhancing the level and scope of molecular marker-assisted breeding for maize improvement in Asia.
Abstract: Maize is one of the most important food and feed crops in Asia, and is a source of income for several million farmers Despite impressive progress made in the last few decades through conventional breeding in the “Asia-7” (China, India, Indonesia, Nepal, Philippines, Thailand, and Vietnam), average maize yields remain low and the demand is expected to increasingly exceed the production in the coming years Molecular marker-assisted breeding is accelerating yield gains in USA and elsewhere, and offers tremendous potential for enhancing the productivity and value of Asian maize germplasm We discuss the importance of such efforts in meeting the growing demand for maize in Asia, and provide examples of the recent use of molecular markers with respect to (i) DNA fingerprinting and genetic diversity analysis of maize germplasm (inbreds and landraces/OPVs), (ii) QTL analysis of important biotic and abiotic stresses, and (iii) marker-assisted selection (MAS) for maize improvement We also highlight the constraints faced by research institutions wishing to adopt the available and emerging molecular technologies, and conclude that innovative models for resource-pooling and intellectual-property-respecting partnerships will be required for enhancing the level and scope of molecular marker-assisted breeding for maize improvement in Asia Scientists must ensure that the tools of molecular marker-assisted breeding are focused on developing commercially viable cultivars, improved to ameliorate the most important constraints to maize production in Asia
TL;DR: The recombinants combining resistance to Septoria tritici blotch, yellow leaf spot, rust diseases and root-lesion nematodes from parents CPI133872 and Janz constitute valuable germplasm for the transfer of multiple disease resistance into new wheat cultivars.
Abstract: A genetic linkage map, based on a cross between the synthetic hexaploid CPI133872 and the bread wheat cultivar Janz, was established using 111 F1-derived doubled haploid lines. The population was phenotyped in multiple years and/or locations for seven disease resistance traits, namely, Septoria tritici blotch (Mycosphaeralla graminicola), yellow leaf spot also known as tan spot (Pyrenophora tritici-repentis), stripe rust (Puccinia striiformis f. sp. tritici), leaf rust (Puccinia triticina), stem rust (Puccinia graminis f. sp. tritici) and two species of root-lesion nematode (Pratylenchyus thornei and P. neglectus). The DH population was also scored for coleoptile colour and the presence of the seedling leaf rust resistance gene Lr24. Implementation of a multiple-QTL model identified a tightly linked cluster of foliar disease resistance QTL in chromosome 3DL. Major QTL each for resistance to Septoria tritici blotch and yellow leaf spot were contributed by the synthetic hexaploid parent CPI133872 and linked in repulsion with the coincident Lr24/Sr24 locus carried by parent Janz. This is the first report of linked QTL for Septoria tritici blotch and yellow leaf spot contributed by the same parent. Additional QTL for yellow leaf spot were detected in 5AS and 5BL. Consistent QTL for stripe rust resistance were identified in chromosomes 1BL, 4BL and 7DS, with the QTL in 7DS corresponding to the Yr18/Lr34 region. Three major QTL for P. thornei resistance (2BS, 6DS, 6DL) and two for P. neglectus resistance (2BS, 6DS) were detected. The recombinants combining resistance to Septoria tritici blotch, yellow leaf spot, rust diseases and root-lesion nematodes from parents CPI133872 and Janz constitute valuable germplasm for the transfer of multiple disease resistance into new wheat cultivars.
TL;DR: In this paper, the location and borders of the alien chromosome segment introgressed from TxAG-6 into NemaTAM (a BC7-derived introgression line) and other modern cultivars carrying Rma have not been genetically mapped.
Abstract: Rma, a dominant root-knot nematode resistance gene introduced into tetraploid peanut (Arachis hypogaea) from a synthetic allotetraploid donor (TxAG-6), has been widely deployed in modern cultivars. The genomic location and borders of the alien chromosome segment introgressed from TxAG-6 into NemaTAM (a BC7-derived introgression line) and other modern cultivars carrying Rma have not been genetically mapped, and resistance gene candidates (RGCs) have not been identified for Rma. Our study focused on densely populating the alien introgression with codominant DNA markers, identifying and mapping the borders of the alien introgression carried by NemaTAM, and identifying RGCs for Rma. Altogether, 2,847 simple sequence repeat (SSR) and 380 single strand conformational polymorphism (SSCP) markers were screened for linkage to Rma-247 of the SSCP markers targeted 202 nucleotide binding site (NBS) leucine-rich repeat (LRR) and other resistance (R) gene homologs (75 were identified by mining a peanut EST database). SSR, NBS-LRR, and Ser/Thr receptor-like protein loci within the alien introgression co-segregated with Rma in an F4 population (Gregory × Tifguard) and were tightly linked and spanned 3.4 cM in an F5 population (NemaTAM × GP-NC-WS-14). By comparative mapping in the A-genome progenitor of peanut (A. duranensis), Rma was discovered to have been introduced on an interstitial alien chromosome segment spanning one-third to one-half of chromosome 9A. Numerous codominant DNA markers were identified for finer mapping of Rma, shortening the alien introgression harboring Rma by marker-assisted selection, and introducing novel root-knot nematode R-genes into peanut by targeting syntenic segments on chromosomes 9A and 9B in wild diploid donors.
TL;DR: A genome wide set of 436 validated highly variable SSR (HvSSR) markers with repeat lengths of 51–70 bp are described for their consistent amplification and high polymorphism and therefore are suitable for QTL mapping and fingerprinting studies in rice employing agarose gels.
Abstract: Simple sequence repeats (SSR) are the DNA markers of choice for genetic analysis in rice (Oryza sativa L.) due to their abundance, high polymorphism and simple assays using agarose gel electrophoresis. In an attempt to find most variable SSR loci for the agarose gel system, the relationship between SSR length and level of polymorphism was evaluated in a set of eight diverse rice genotypes using 201 random SSR loci of different repeat motifs and lengths, representing both genic and intergenic sequences from the 12 rice chromosomes. There was a positive correlation between SSR length and average number of alleles per locus but linearity of this relationship was limited to the SSR length range of 10–70 bp. The highest level of polymorphism was in the SSR length range of 51–70 bp, beyond which there was stabilization and then decline of polymorphism in SSRs longer than 70 bp. Proportion of polymorphic loci in the different SSR length groups also followed similar pattern with even sharper decline of polymorphism in the highest size range. Here we describe a genome wide set of 436 validated highly variable SSR (HvSSR) markers with repeat lengths of 51–70 bp for their consistent amplification and high polymorphism. In the parental lines of three different mapping populations, the HvSSR loci showed more than twice the level of polymorphism than random SSR markers with average repeat length of 34 bp, and therefore are suitable for QTL mapping and fingerprinting studies in rice employing agarose gels.
TL;DR: This study reports the changes in proteome of soybean seeds exposed to low temperature (4°C) during imbibition in a known chilling-resistant soybean cultivar Z22, using two-dimensional gel electrophoresis (2-DE) and Matrix-Assisted Laser Ionization Time of Flight Mass Spectrometry (MALDI-TOF/MS).
Abstract: Many of the world’s important crops such as soybean are now widely distributed, beyond their original zones of natural selection and chilling temperature is one of the major abiotic environmental factors which limit their growth and yield. Various molecular mechanisms, underlying chilling stress and plant responses are yet to be discovered. Chilling temperatures impart maximum damage to the soybean seeds, sown in wet soils, during imbibition, causing poor germination rate, reduced seedling emergence, decreased seedling vigor, and ultimately severe loss in yield. Here we report the changes in proteome of soybean seeds exposed to low temperature (4°C) during imbibition in a known chilling-resistant soybean cultivar Z22, using two-dimensional gel electrophoresis (2-DE) and Matrix-Assisted Laser Ionization Time of Flight Mass Spectrometry (MALDI-TOF/MS). Total 40 protein spots were differentially expressed in response to low temperature, in which, 25 protein spots were up-regulated and fifteen protein spots were down-regulated. According to the search in primary databases, these proteins were a part of many metabolic pathways including, cell defense, energy, protein synthesis, cell growth/division, storage, transcription and transport. To investigate the change in mRNA levels during imbibition at 4°C, quantitative RT-PCR of nine up-regulated protein genes was carried out, which clearly demonstrated an increase in the transcript levels of five genes, whereas no change was observed for other four genes. Results of this study provide some invaluable insights about the response of soybean seeds to low temperature imbibition which include; (1) alcohol dehydrogenase I and RAB21 might contribute in decreasing the effect of anoxia, resulting from water up-take during imbibition, (2) stress-related proteins such as LEA and GST24 probably played a pivotal role in confronting low temperature stress and (3) expression of some crucial enzymes (malate dehydrogenase and phosphoenolpyruvate carboxylase) involved in TCA cycle was enhanced, which might be beneficial for seeds, in stress conditions during germination.
TL;DR: In this work, an EMS-mutagenised population of bread wheat cv.
Abstract: Given the important role that starch plays in food and non-food uses of many crops, particularly wheat, efforts are being made to manipulate its composition through modification of the amylose/amylopectin ratio. Approaches used to achieve this goal include the manipulation of the genes involved in the starch biosynthetic pathway using natural or induced mutations and transgenic methods. The use of mutagenesis to produce novel allelic variation represents a powerful tool to increase genetic diversity and this approach seems particularly appropriate for starch synthase genes for which limited variation exists. In this work, an EMS-mutagenised population of bread wheat cv. Cadenza has been screened by combining SDS–PAGE analysis of granule bound starch proteins with a TILLING (Targeting Induced Local Lesions IN Genomes) approach at the gene level. In particular we have focused on two groups of synthase genes, those encoding the starch synthase II (Sgp-1) and those corresponding to the waxy proteins (Wx). SDS–PAGE analysis of granule bound proteins allowed the identification of single null genotypes associated with each of the three homoeologous loci. Molecular characterization of induced mutants has been performed using genome specific primer pairs for Sgp-1 and Wx genes. Additional novel allelic variation has also been detected at the different Sgp-1 homoeoloci by using a reverse genetic approach (TILLING). In particular single nucleotide substitutions, introducing a premature stop codon and creating amino acid substitutions, have been identified.
TL;DR: Durum wheat accessions suitable for association mapping has been tested for leaf rust response at the seedling stage and under field conditions (adult plant stage), and the chr.
Abstract: Resistance to leaf rust (Puccinia triticina Eriks.) is a main objective for durum wheat (Triticum durum Desf.) breeding. Association mapping on germplasm collections is now being used as an additional approach for the discovery and validation of major genes/QTLs. In this study, a collection of 164 elite durum wheat accessions suitable for association mapping has been tested for leaf rust response at the seedling stage and under field conditions (adult plant stage). Seedling tests were carried out with 25 selected isolates from durum wheat, bread wheat and triticale, while field experiments were carried out in artificially inoculated plots in Italy and in Mexico. The collection has been profiled with 225 simple sequence repeat (SSR) loci of known map position and a PCR assay targeting Ppd-A1. Associations showing highly consistent experiment-wise significances across leaf rust isolates and field trials were mainly detected for the 7BL distal chromosome (chr.) region (harbouring Lr14 from cultivar Llareta INIA and QLr.ubo-7B.2 from cultivar Creso) and for two chr. regions located in chrs. 2A and 2B. Additionally, isolate-specific associations and/or associations with smaller effects in the field trials were identified in most of the chromosomes. The chr. 7BL distal region was investigated in detail through haplotyping with 15 SSR markers, revealing that the Creso and Llareta INIA alleles are identical by descent at 6 adjacent SSR loci in the most distal 7BL region spanning 8 cM. Association mapping allowed us to further refine the map location of the Lr14/QLr.ubo-7B.2 resistance gene to the most distal region of the linkage group, tagged by Xcfa2257.2, Xgwm344.2 and Xwmc10. The resistant haplotype is present in a number of accessions (ca. 15% of the accessions included in the collection) from the Italian, CIMMYT and ICARDA breeding programmes. Therefore, this chr. 7BL region can be considered as the most important source of resistance to leaf rust currently exploited by durum breeders in the Mediterranean areas. Furthermore, the field trials at the adult plant stage allowed us to identify marker associations (e.g. chrs. 2BL and 3BS, proximal regions; chr. 7BS, distal region) which suggest the presence of minor QTLs for slow-rusting resistance.
TL;DR: With the integration of 282 new markers into the common bean core map, the authors were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust.
Abstract: Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the ‘BAT93’ × ‘Jalo EEP558’ cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.
TL;DR: A breeding-to-genetics approach is proposed, which starts with identification of extreme phenotypes from segregating populations generated from multiple parental lines and is followed by rapid discovery of individual genes and combinations of gene effects together with simultaneous manipulation in breeding programs.
Abstract: Selective genotyping of individuals from the two tails of the phenotypic distribution of a population provides a cost efficient alternative to analysis of the entire population for genetic mapping. Past applications of this approach have been confounded by the small size of entire and tail populations, and insufficient marker density, which result in a high probability of false positives in the detection of quantitative trait loci (QTL). We studied the effect of these factors on the power of QTL detection by simulation of mapping experiments using population sizes of up to 3,000 individuals and tail population sizes of various proportions, and marker densities up to one marker per centiMorgan using complex genetic models including QTL linkage and epistasis. The results indicate that QTL mapping based on selective genotyping is more powerful than simple interval mapping but less powerful than inclusive composite interval mapping. Selective genotyping can be used, along with pooled DNA analysis, to replace genotyping the entire population, for mapping QTL with relatively small effects, as well as linked and interacting QTL. Using diverse germplasm including all available genetics and breeding materials, it is theoretically possible to develop an “all-in-one plate” approach where one 384-well plate could be designed to map almost all agronomic traits of importance in a crop species. Selective genotyping can also be used for genomewide association mapping where it can be integrated with selective phenotyping approaches. We also propose a breeding-to-genetics approach, which starts with identification of extreme phenotypes from segregating populations generated from multiple parental lines and is followed by rapid discovery of individual genes and combinations of gene effects together with simultaneous manipulation in breeding programs.
TL;DR: It is anticipated that molecular diversity information generated on parental lines of hybrids under development, and identification of the two most suitable markers for testing the purity of hybrid seeds of ICPH 2438, will facilitate the pigeonpea hybrid breeding programme.
Abstract: With an objective of achieving a breakthrough in the productivity of pigeonpea, a hybrid breeding technology based on elements of the cytoplasmic-nuclear male-sterility (CMS) system and partial natural out-crossing has recently been developed. However, there is no molecular diversity information available on parental lines of hybrids being generated at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). This study deals with the use of 148 simple sequence repeat (SSR) markers, including 32 novel markers reported here for the first time, on 159 A (cytoplasmic male sterile), B (maintainer) and R (fertility restorer) lines. In total, 41 (27.7%) markers showed polymorphism with 2 to 6 (average 2.6) alleles and 0.01 to 0.81 (average 0.34) polymorphism information content (PIC) value. Of these polymorphic markers, 22 SSR markers showed polymorphism between A (ICPA 2039) and R (ICPR 2438) lines of the commercial hybrid (ICPH 2438); however, only 21 of these SSR markers showed the same profile between A (ICPA 2039) and B (ICPB 2039) lines. Finally, two SSR markers, CCB4 and CCttc006, were found most suitable for purity assessment of hybrid seeds of the ICPH 2438 hybrid. The utility of these two diagnostic SSR markers has been demonstrated by using seed lots of this hybrid from two sources, ICRISAT and Mahabeej. It is anticipated that molecular diversity information generated on parental lines of hybrids under development, and identification of the two most suitable markers for testing the purity of hybrid seeds of ICPH 2438, will facilitate the pigeonpea hybrid breeding programme.
TL;DR: To identify quantitative trait loci (QTLs) for spot blotch resistance, two mapping populations were developed by making the crosses between common susceptible cultivar ‘Sonalika’ with the resistant breeding lines ‘Ning 8201’ and ‘Chirya 3’.
Abstract: Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat in warm and humid wheat growing regions of the world. To identify quantitative trait loci (QTLs) for spot blotch resistance, two mapping populations were developed by making the crosses between common susceptible cultivar ‘Sonalika’ with the resistant breeding lines ‘Ning 8201’ and ‘Chirya 3’. Single seed descent derived F6, F7, F8 lines of the first cross ‘Ning 8201’ × ‘Sonalika’ were evaluated for resistance to spot blotch in three blocks in each of the 3 years. After screening of 388 pairs of simple sequence repeat primers between the two parents, 119 polymorphic markers were used to genotype the mapping population. Four QTLs were identified on the chromosomes 2AS, 2BS, 5BL and 7DS and explained 62.9% of phenotypic variation in a simultaneous fit. The QTL on chromosome 2A was detected only in 1 year and explained 22.7% of phenotypic variation. In the second cross (‘Chirya 3’ × ‘Sonalika’), F7 and F8 population were evaluated in three blocks in each of the 2 years. In this population, five QTLs were identified on chromosomes 2BS, 2DS, 3BS, 7BS and 7DS. The QTLs identified in the ‘Chirya 3’ × ‘Sonalika’ population explained 43.4% of phenotypic variation in a simultaneous fit. The alleles for reduced disease severity in both the populations were derived from the respective resistant parent. The QTLs QSb.bhu-2B and QSb.bhu-7D from both populations were placed in the same deletion bins, 2BS1-0.53-0.75 and 7DS5-0.36-0.61, respectively. The closely linked markers Xgwm148 to the QTL on chromosome 2B and Xgwm111 to the QTL on chromosome 7D are potentially diagnostic markers for spot blotch resistance.
TL;DR: The findings suggest that through the appropriate combination of alleles at these three loci one would be able to regulate the various developmental phases to accommodate different agricultural needs.
Abstract: The orderly development of winter wheat through its life cycle can be marked at three stages: stem elongation, heading date, and physiological maturity. The duration of a developmental phase between two stages is important in yield component generation. In this study the three developmental stages were characterized and 350 markers were mapped in a population of recombinant inbred lines (RILs) generated from a cross between two winter wheat cultivars (‘Jagger’ and ‘2174’). Three major QTLs were found to control variation in developmental process, and each of them was tightly associated with a known flowering gene, VRN-A1 on chromosome 5A, PPD-D1 on chromosome 2D, and VRN-D3 on chromosome 7D. The average contribution of the gene marker for each QTL to the total phenotypic variation (R2) was evaluated over 3 years. The effect of VRN-A1 ranged from 21.5% at stem elongation to 17.4% at physiological maturity. The effect of PPD-D1 was minor (6.7%) at stem elongation but increased to 29.7% at heading and 20.1% at physiological maturity. The effect of VRN-D3 was not detected at stem elongation but increased to 14.6% at heading and to 20.5% at physiological maturity. Hence, the VRN-A1 locus, the PPD-D1 locus, and the VRN-D3 locus had greatest impact on development at stem elongation, heading date, and physiological maturity, respectively. Whereas the Jagger VRN-A1 and VRN-D3 alleles accelerated development, the Jagger PPD-D1 allele delayed the developmental process due to its sensitivity to photoperiod. Our findings suggest that through the appropriate combination of alleles at these three loci one would be able to regulate the various developmental phases to accommodate different agricultural needs.
TL;DR: The tetraploid wheat doubled haploid population and genetic maps reported here will be useful for genetic dissection of important agronomic traits as well as the identification and development of markers for marker-assisted selection (MAS).
Abstract: Durum wheat (Triticum turgidum L. subsp. durum, 2n = 4x = 28, AABB) is an important cereal used for making pasta products. Compared with bread wheat, durum wheat receives less attention in genetic and genomic studies. In this research, a tetraploid wheat doubled haploid (DH) population derived from the cross between the durum wheat cultivar ‘Lebsock’ and the T. turgidum subsp. carthlicum (2n = 4x = 28, AABB) accession PI 94749 was developed. The population consisted of 146 lines and was used to construct linkage maps of all 14 chromosomes. The maps consisted of 280 SSR markers and spanned 2,034.1 cM with an average density of one marker per 7.2 cM. The DH population and the whole genome linkage maps were then used to identify QTLs associated with tan spot resistance. The DH population was inoculated separately with two Ptr ToxA-producing isolates (Pti2 and 86-124) representing races 1 and 2, respectively, of Pyrenophora tritici-repentis, and five resistance QTLs were detected on chromosome arms 3AS, 3BL, 5AL and 7BL. Together, the QTLs explained a total of 46 and 41% of the phenotypic variation for reaction to Pti2 and 86-124, respectively. The Tsn1-Ptr ToxA interaction was not a significant factor in tan spot development in this population, and none of the QTLs corresponded to previously identified loci known to confer insensitivity to host-selective toxins (HSTs) produced by P. tritici-repentis. This result, together with those of other similar studies, indicates that the wheat–P. tritici-repentis pathosystem involves more factors than currently published host-toxin interactions. The DH population and genetic maps reported here will be useful for genetic dissection of important agronomic traits as well as the identification and development of markers for marker-assisted selection (MAS).
TL;DR: The identification of molecular markers linked to the resistance would allow tracking of the underlying genes, facilitating their introgression into pea cultivars and the identification of genomic regions associated with resistance to O. crenata is identified.
Abstract: Crenate broomrape (Orobanche crenata) is the major constraint for pea cultivation in the Mediterranean Basin and Middle East. Cultivation of resistant varieties would be the most efficient, economical and environmentally friendly way to control this parasite. However, little resistance is available within cultivated pea. Promising sources of resistance have been identified in wild peas but their use in breeding programs is hampered by the polygenic nature of the resistance. The identification of molecular markers linked to the resistance would allow tracking of the underlying genes, facilitating their introgression into pea cultivars. The main objective of this study was the identification of genomic regions associated with resistance to O. crenata. A RIL (Recombinant Inbred Lines) population derived from a cross between a resistant accession of the wild pea Pisum sativum ssp. syriacum, and a susceptible pea variety was screened for resistance to O. crenata under field conditions during two seasons. In addition, resistance reactions at different stages of the O. crenata infection cycle were assessed using a Petri dish method. The approach allowed the identification of four Quantitative Trait Loci (QTL) associated with field resistance, assessed as the number of emerged broomrape shoots per pea plant under field conditions. These identified QTLs explained individually from 10 to 17% of the phenotypic variation. In addition QTLs governing specific mechanisms of resistance, such as low induction of O. crenata seed germination, lower number of established tubercles per host root length unit, and slower development of tubercles were also identified. Identified QTLs explained individually from 8 to 37% of the variation observed depending on the trait. Host plant aerial biomass and root length were also assessed and mapped. Both traits were correlated with the level of O. crenata infection and three out of the four QTLs controlling resistance under field conditions co-localized with QTLs controlling plant aerial biomass or root length. The relationship observed among these traits and resistance is discussed.
TL;DR: A pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform is developed.
Abstract: Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation.
TL;DR: The development and transferability of simple sequence repeat (SSR) markers, over 40% of which are EST-derived, from ssp.
Abstract: Asparagus bean (V. unguiculata ssp. sesquipedialis), a specific form of cowpea (V. unguiculata L. Walp.), is cultivated as a vegetable crop throughout eastern and southern Asia for its tender long pods. Little is known about the genetic relationship between asparagus bean and the broader species, particularly the dominant ssp. unguiculata. We report here the development and transferability of simple sequence repeat (SSR) markers, over 40% of which are EST-derived, from ssp. unguiculata to asparagus bean and the use of a subset of the polymorphic markers to assess the genetic diversity of asparagus bean cultivars from diverse geographic origins across China. A total of 410 EST derived SSR (eSSR) markers and 600 SSR markers derived from cowpea genespace sequences (GSS) were developed, with a cross-subspecies transferability of 100% and 98.5%, respectively. In a recombinant inbred line population of asparagus bean, a 1:1 segregation was observed for most loci. Principal coordinate analysis (PCA) and phylogenetic clustering based on 62 alleles detected by 14 polymorphic SSR markers distinguished ssp. unguiculata and sesquipedialis into separate groups. Improved asparagus bean cultivars in China generally have a narrow genetic basis compared with landraces varieties. This suggests that asparagus bean breeding programs need to consider utilizing landrace germplasm to enhance genetic variability and ensure long-term gains from selection and reduce genetic vulnerability to pathogen/pest epidemics. Because of their transferability across subspecies, the SSR markers described in this study could be effectively employed in cross-subspecies trait introgression breeding from ssp. unguiculata to sesquipedialis.
TL;DR: The first principal component of elliptic Fourier descriptors, accounting for over 90% of the total variation, was associated with the length:width ratio of brown rice.
Abstract: Although grain shape is an important cereal breeding target, it has only been evaluated using simple measurements, e.g., the length:width ratio. We used elliptic Fourier analysis to evaluate grain shape variation and conducted whole genome association mapping of grain shape using a germplasm collection of Asian cultivated rice. The first principal component of elliptic Fourier descriptors, accounting for over 90% of the total variation, was associated with the length:width ratio of brown rice. That component was the most significant among the first ten components: the length:width ratio is the major genetic variation of rice grain shape. Bayesian multilocus association mapping detected five significant markers for this component; three might be linked to previously reported quantitative trait loci. Allelic effects of significant markers were visualized using inverse Fourier transformation, showing that the allele of a Japonica variety “Nipponbare” produced plumper grains in four of five significant markers. For the second to tenth principal components, varietal effects were significant (P < 0.001), although most accounted for less than 1% of the total variation in elliptic Fourier descriptors. Association mapping detected at least one quantitative trait locus in six of these nine components: breeding programs can improve the heritable shape characteristics associated with these components. For association mapping, elliptic Fourier analysis’ accuracy and high throughput are suitable; it is readily applicable to cereal crops because it is not based on rice-specific morphological characteristics but rather on universal shape descriptors that can delineate any closed contour.
TL;DR: Assays developed for four of the five target genes are suitable for marker-assisted selection in potato breeding programs and further advances in the technology and associated data analysis should make HRM a useful tool for basic and applied studies of potato.
Abstract: The ideal marker system for tetraploid potato would be dosage-sensitive and have the ability to distinguish heterozygous genotypes with multiple haplotypes within the genomic region targeted by the marker. The objective of this study was to evaluate the utility of high-resolution DNA melting (HRM) for genotyping and polymorphism detection in diploid and tetraploid potato. Amplicon scanning, unlabelled probe, and short amplicon assays were developed for four candidate genes affecting tuber skin and flesh colour, and starch, and a marker linked to nematode resistance. Genotyping a set of 95 potato clones revealed several examples of clones with three distinct haplotypes. Combined probe and amplicon analysis identified between 29 and 44 unique genotypes for the same assays. Assays developed for four of the five target genes are suitable for marker-assisted selection in potato breeding programs. This study illustrates the use of HRM in potato genetics. Further advances in the technology and associated data analysis should make HRM a useful tool for basic and applied studies of potato.
TL;DR: An attempt to use a whole-genome scan with DArT markers to identify chromosomal regions influencing LMA in synthetic hexaploid wheat (SHW) finds a region on chromosome 6B, which was identified as having a significant association with LMA phenotypes in the SHW accessions.
Abstract: Late maturity α-amylase (LMA) is a genetic defect of wheat which results in the production of α-amylase, shown as substandard falling numbers, in the absence of preharvest rain and under cool temperatures during ripening. The present study is an attempt to use a whole-genome scan with DArT markers to identify chromosomal regions influencing LMA in synthetic hexaploid wheat (SHW). A high heritability estimate of 86.6% was calculated for LMA phenotype measured as optical density in a collection of 91 SHWs. Linkage disequilibrium extended up to 10 cM, and with controls for false positives, significant markers were detected at the chromosome 7B region previously linked to LMA in bread wheat, but not at the chromosome 3B region. Of potentially great interest is a region on chromosome 6B, which was identified as having a significant association with LMA phenotypes in the SHW accessions. Previous investigations suggested existence of an LMA gene on the long arm of 6B, but this is the first time it has been mapped to lie within the centromeric region of chromosome 6B, a region that harbours the Amy-1 genes and whose expression governs activity of the high pI α-amylase isoenzymes.
TL;DR: The consensus map could be the starting point for the identification and the cloning of major genes and QTL in fundamental and applied genetic areas in chicory.
Abstract: A consensus genetic map for chicory (2n = 2x = 18) was obtained after the integration of molecular marker data of two industrial chicory progenies (K28K59, Rubis118) and one witloof chicory progeny (BR). As a limited number of co-dominant markers was available at the beginning of this work, three different microsatellite-enriched libraries were produced from genomic DNA, resulting in 420, 719 and 1,251 sequences, respectively. The level of informative Simple Sequence Repeat (SSR) sequences from the three libraries ranged from 28 to 40%, thus defining a set of 730 SSR markers available for polymorphism screening. A subset of 81 Sequence-Tagged Sites (STS) developed from EST, cDNA, genes, and non-coding sequences was screened through Single Strand Conformational Polymorphism (SSCP) analysis, leading to 46 polymorphic loci integrated in the genetic maps. Markers were grouped and ordered on 9 homologous Linkage Groups (LG) for each of the three maps: 274 markers in K28K59, 282 markers in Rubis118, 178 markers in BR. Co-linear regions between maps were identified through 193 ‘bridge’ markers that allowed the integration of the 9 homologous LG in a consensus map containing 472 markers and covering 878 cM. Comparison across maps revealed the presence of 4 conserved regions with significant distorted markers, also defined as Segregation Distortion Regions (SDR), affected by gametic or zygotic selection factors. Marker distribution was not always uniform; 6 LG possessed homologous clustered regions in all maps. The consensus map could be the starting point for the identification and the cloning of major genes and QTL in fundamental and applied genetic areas in chicory.