Showing papers on "Plant breeding published in 2015"

Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

Abstract: Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

MutMap accelerates breeding of a salt-tolerant rice cultivar

Abstract: 445 two chromosome substitution lines (CSSLs), SL502 and SL503, harboring chromosomal segments of Nona Bokra in the genetic background of Koshihikari, a cultivar closely related to Hitomebore10,11. We compared the growth of hst1, SL502 and SL503 at 0.75% NaCl (Supplementary Fig. 2). The 18 and 43% improved growth of hst1 as compared to SL503 and SL502, respectively, showed that this was a good starting point for breeding a salt-tolerant rice cultivar. For rapid identification of the mutation conferring salinity tolerance in hst1, we used MutMap, a method based on wholegenome resequencing of bulked DNA of F2 segregants1. The hst1 line was crossed to WT Hitomebore to generate F1 progeny, and F2 progeny were derived from self-pollination of the F1 progeny. Two-week-old F2 seedlings were treated with water containing 0.75% NaCl. The progeny segregated in a 133:54 ratio for salinity-susceptible and salinitytolerant phenotypes, respectively, conforming to a 3:1 segregation ratio (chi-squared test: χ2 = 2.2 × 10-16, nonsignificant) and thereby indicating that the salinity tolerance of hst1 is conferred by a single recessive mutation. We combined DNA from 20 F2 progeny that had the salinity-tolerance phenotype and applied whole-genome resequencing using an Illumina GAIIx DNA sequencer. We obtained a total of 7.34 Gbp of short (75-bp) reads (Supplementary Table 1) that were aligned to the Hitomebore reference sequence (DDBJ Sequence Read Archive DRA000927), resulting in the identification of 1,005 SNP positions. For each SNP position, the value of SNP-index (the ratio of short reads harboring SNPs different from the reference1) was obtained and a graph relating SNP positions and SNP-index was generated for all 12 rice chromosomes (Fig. 2a, Supplementary Fig. 3). The causative SNP should be shared by all the mutant F2 plants and therefore have a SNP-index = 1, whereas SNPs unrelated to the mutant phenotype should segregate in a 1:1 ratio among the F2 progeny, resulting in a SNP-index of ~0.5. MutMap applied to hst1 To the Editor: Following the 2011 earthquake and tsunami that affected Japan, >20,000 ha of rice paddy field was inundated with seawater, resulting in salt contamination of the land. As local rice landraces are not tolerant of high salt concentrations, we set out to develop a salttolerant rice cultivar. We screened 6,000 ethyl methanesulfonate (EMS) mutant lines of a local elite cultivar, ‘Hitomebore’, and identified a salt-tolerant mutant that we name hitomebore salt tolerant 1 (hst1). In this Correspondence, we report how we used our MutMap method1 to rapidly identify a loss-of-function mutation responsible for the salt tolerance of hst1 rice. The salttolerant hst1 mutant was used to breed a salt-tolerant variety named ‘Kaijin’, which differs from Hitomebore by only 201 singlenucleotide polymorphisms (SNPs). Field trials showed that it has the same growth and yield performance as the parental line under normal growth conditions. Notably, production of this salt-tolerant mutant line ready for delivery to farmers took only two years using our approach. Although soluble salts, such as nitrates and potassium salts, are common components of soil and essential plant nutrients, their accumulation above specific threshold concentrations can substantially affect plant growth. There is considerable variation among plants with respect to their tolerance of salinity, and rice is considered the most sensitive of all the cereals2. Yields of paddy rice start to decline at salinity levels >3 dS m–1 (measured by the electrical conductivity of the extract, ECe), beyond which a 12% reduction in yield is expected for every 1 dS m–1 increase in ECe. Soil salinity affects >6% of world’s total land area, causing yield losses as a result of both osmotic and ionic stresses to crop plants2. Soil salinization due to the flooding of agricultural lands by seawater has become an additional concern since the 2004 Indian Ocean tsunami4. In 2011, Japan was hit by the Great Tohoku Earthquake, which triggered a devastating tsunami, altogether claiming the lives of more than 15,000 people. The tsunami extended more than 5 km inland on the Sendai Plain of Miyagi Prefecture, one of the main rice-production regions in Japan5. An environmental impact assessment study conducted in the same area over a period of 2–7 months after the tsunami revealed wide spatial variation in the salinity level of ponded water, with ECe ranging from 0.31 to 68.2 mS cm–1 (ref. 6). Although salt concentration gradually decreased, it was too high for rice production to resume in October, 2011. To restore rice production in tsunamiaffected areas of the Tohoku region of Japan, we set out to develop and deliver a salt-tolerant rice cultivar from a line suited to local agronomic conditions. First, we carried out a genetic screen for salt tolerance using seeds pooled from approximately 6,000 independent EMS-mutagenized lines of Hitomebore7, (Supplementary Fig. 1). We identified a mutant that survived with 1.5% NaCl supplied to the soil with irrigation water for 7 days, which we designated hitomebore salt tolerant 1 (hst1). Seeds from a self-pollinated hst1 plant were used to further test the performance of hst1 at different NaCl concentrations (Fig. 1a,b). The hst1 mutant grew better than wild-type (WT) Hitomebore plants at both 0.375% and 0.75% NaCl concentrations, as measured after 14 days of treatment. The 0.375% NaCl treatment caused reductions of 38.4% and 2.9% in the fresh weight of WT and hst1 plants, respectively. At 0.75% NaCl, WT plants dried out, with a 61.5% reduction in fresh weight, whereas hst1 plants remained green with only a 13.2% reduction in fresh weight compared with hst1 plants that received fresh water (Fig. 1b). Previously, the rice SHOOT K+ CONCENTRATION 1 (SKC1) gene, encoding a Na+ transporter, was identified as the main quantitative trait locus (QTL) conferring salt tolerance in the indica cultivar Nona Bokra8,9. This QTL has been used to develop MutMap accelerates breeding of a salt-tolerant rice cultivar CORRESPONDENCE

Genome-Wide Linkage Mapping of QTL for Yield Components, Plant Height and Yield-Related Physiological Traits in the Chinese Wheat Cross Zhou 8425B/Chinese Spring.

Abstract: Identification of genes for yield components, plant height and yield-related physiological traits and tightly linked molecular markers is of great importance in marker-assisted selection (MAS) in wheat breeding. In the present study, 246 F8 RILs derived from the cross of Zhou 8425B/Chinese Spring were genotyped using the high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay. Field trials were conducted at Zhengzhou and Zhoukou of Henan Province, during the 2012–2013 and 2013–2014 cropping season sunder irrigated conditions, providing data for four environments. Analysis of variance (ANOVA) of agronomic and physiological traits revealed significant differences (P<0.01) among RILs, environments, and RIL × environment interactions. Broad-sense heritabilities of all traits including thousand kernel weight (TKW), plant height (PH), spike length (SL), kernel number per spike (KNS), spike number/m2 (SN), normalized difference in vegetation index at anthesis (NDVI-A) and at 10 days post-anthesis (NDVI-10), SPAD value of chlorophyll content at anthesis (Chl-A) and at 10 days post-anthesis (Chl-10) ranged between 0.65 and 0.94. A linkage map spanning 3,609.4 cM was constructed using 5,636 polymorphic SNP markers, with an average chromosome length of 171.9 cM and marker density of 0.64 cM/marker. A total of 866 SNP markers were newly mapped to the hexaploid wheat linkage map. Eighty-six QTL for yield components, plant height and yield-related physiological traits were detected on 18 chromosomes except 1D, 5D and 6D, explaining 2.3 to 33.2% of the phenotypic variance. Ten stable QTL were identified across four environments, viz. QTKW.caas-6A.1, QTKW.caas-7AL, QKNS.caas-4AL, QSN.caas-1AL.1, QPH.caas-4BS.2, QPH.caas-4DS.1, QSL.caas-4AS, QSL.caas-4AL.1, QChl-A.caas-5AL and QChl-10.caas-5BL. Meanwhile, 10 QTL-rich regions were found on chromosome 1BS, 2AL (2), 3AL, 4AL (2), 4BS, 4DS, 5BL and 7AL exhibiting pleiotropic effects. These QTL or QTL clusters are tightly linked to SNP markers, with genetic distances to the closest SNPs ranging from 0 to 1.5 cM, and could serve as target regions for fine mapping, candidate gene discovery, and marker-assisted selection in wheat breeding.

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

Abstract: Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.

Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

Abstract: Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

Genome-Wide Association Mapping of Yield and Grain Quality Traits in Winter Wheat Genotypes.

Abstract: The main goal of this study was to investigate the genetic basis of yield and grain quality traits in winter wheat genotypes using association mapping approach, and identify linked molecular markers for marker assisted selection. A total of 120 elite facultative/winter wheat genotypes were evaluated for yield, quality and other agronomic traits under rain-fed and irrigated conditions for two years (2011–2012) at the Tel Hadya station of ICARDA, Syria. The same genotypes were genotyped using 3,051 Diversity Array Technologies (DArT) markers, of which 1,586 were of known chromosome positions. The grain yield performance of the genotypes was highly significant both in rain-fed and irrigated sites. Average yield of the genotypes ranged from 2295 to 4038 kg/ha and 4268 to 7102 kg/ha under rain-fed and irrigated conditions, respectively. Protein content and alveograph strength (W) ranged from 13.6–16.1% and 217.6–375 Jx10-4, respectively. DArT markers wPt731910 (3B), wPt4680 (4A), wPt3509 (5A), wPt8183 (6B), and wPt0298 (2D) were significantly associated with yield under rain-fed conditions. Under irrigated condition, tPt4125 on chromosome 2B was significantly associated with yield explaining about 13% of the variation. Markers wPt2607 and wPt1482 on 5B were highly associated with protein content and alveograph strength explaining 16 and 14% of the variations, respectively. The elite genotypes have been distributed to many countries using ICARDA’s International system for potential direct release and/or use as parents after local adaptation trials by the NARSs of respective countries. The QTLs identified in this study are recommended to be used for marker assisted selection after through validation using bi-parental populations.

Variations in CYP78A13 coding region influence grain size and yield in rice.

Abstract: Grain size is one of the most important determinants of crop yield in cereals. Here, we identified a dominant mutant, big grain2 (bg2-D) from our enhancer-trapping population. Genetic analysis and SiteFinding PCR (polymerase chain reaction) revealed that BG2 encodes a cytochrome P450, OsCYP78A13. Sequence search revealed that CYP78A13 has a paralogue Grain Length 3.2 (GL3.2, LOC_Os03g30420) in rice with distinct expression patterns, analysis of transgenic plants harbouring either CYP78A13 or GL3.2 showed that both can promote grain growth. Sequence polymorphism analysis with 1529 rice varieties showed that the nucleotide diversity at CYP78A13 gene body and the 20 kb flanking region in the indica varieties were markedly higher than those in japonica varieties. Further, comparison of the genomic sequence of CYP78A13 in the japonica cultivar Nipponbare and the indica cultivar 9311 showed that there were three InDels in the promoter region and eight SNPs (single nucleotide polymorphism) in its coding sequence. Detailed examination of the transgenic plants with chimaeric constructs suggested that variation in CYP78A13 coding region is responsible for the variation of grain yield. Taken together, our results suggest that the variations in CYP78A13 in the indica varieties hold potential in rice breeding for application of grain yield improvement.

Genome wide association study for drought, aflatoxin resistance, and important agronomic traits of maize hybrids in the sub-tropics.

Abstract: The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5–10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.

Genomic Prediction of Biomass Yield in Two Selection Cycles of a Tetraploid Alfalfa Breeding Population.

Abstract: Alfalfa (Medicago sativa L.) is a widely planted perennial forage legume grown throughout temperate and dry subtropical regions in the world. Long breeding cycles limit genetic improvement of alfalfa, particularly for complex traits such as biomass yield. Genomic selection (GS), based on predicted breeding values obtained using genome-wide molecular markers, could enhance breeding efficiency in terms of gain per unit time and cost. In this study, we genotyped tetraploid alfalfa plants that had previously been evaluated for yield during two cycles of phenotypic selection using genotyping-by-sequencing (GBS). We then developed prediction equations using yield data from three locations. Approximately 10,000 single nucleotide polymorphism (SNP) markers were used for GS modeling. The genomic prediction accuracy of total biomass yield ranged from 0.34 to 0.51 for the Cycle 0 population and from 0.21 to 0.66 for the Cycle 1 population, depending on the location. The GS model developed using Cycle 0 as the training population in predicting total biomass yield in Cycle 1 resulted in accuracies up to 0.40. Both genotype × environment interaction and the number of harvests and years used to generate yield phenotypes had effects on prediction accuracy across generations and locations, Based on our results, the selection efficiency per unit time for GS is higher than phenotypic selection, although accuracies will likely decline across multiple selection cycles. This study provided evidence that GS can accelerate genetic gain in alfalfa for biomass yield.

Advances in plant breeding strategies: Breeding, biotechnology and molecular tools

Abstract: The domestication of plants, as a bio-cultural process, is a continuous phenomenon intrinsically associated with the use of plants. Traditional and scientifi c knowledge constitute the basis of the various uses of plants from in situ harvesting to complete domestication of crops. One of the most important challenges of our time is to achieve the conservation and sustainable use of plant genetic resources of landraces, species in the process of domestication and species used in situ. The in situ conservation of agricultural biodiversity is a basic element for the development of more sustainable agroecosystems, the adaptation to climate change, the conservation of ecosystem services and to ensure local food security—a conception that is strongly linked to the local development and the protection of cultural and biological diversity. Through case studies from the Pampa Biome we will discuss the valorization of plant genetic resources through new domestication, the promotion of the use of scientifi cally developed best management practices for in situ conservation, the widening of the germplasm base for breeding programs, plant breeding for stress tolerance, the development of participatory plant breeding programs and the development of high quality products.

Mapping Consistent Rice (Oryza sativa L.) Yield QTLs under Drought Stress in Target Rainfed Environments

Abstract: Drought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target production environments, as well as across different genetic backgrounds, will help to develop high-yielding rice cultivars suitable for water-limited environments through marker-assisted breeding (MAB). Considerable progress has been made in mapping QTLs for drought resistance traits in rice; however, few have been successfully used in MAB. Recombinant inbred lines of IR20 × Nootripathu, two indica cultivars adapted to rainfed target populations of environments (TPEs), were evaluated in one and two seasons under managed stress and in a rainfed target drought stress environment, respectively. In the managed stress environment, the severity of the stress meant that measurements could be made only on secondary traits and biomass. In the target environment, the lines experienced varying timings, durations, and intensities of drought stress. The rice recombinant inbred lines exhibited significant genotypic variation for physio-morphological, phenological, and plant production traits under drought. Nine and 24 QTLs for physio-morphological and plant production traits were identified in managed and natural drought stress conditions in the TPEs, respectively. Yield QTLs that were consistent in the target environment over seasons were identified on chromosomes 1, 4, and 6, which could stabilize the productivity in high-yielding rice lines in a water-limited rainfed ecosystem. These yield QTLs also govern highly heritable key secondary traits, such as leaf drying, canopy temperature, panicle harvest index and harvest index. Three QTL regions on chromosome 1 (RM8085), chromosome 4 (I12S), and chromosome 6 (RM6836) harbor significant additive QTLs for various physiological and yield traits under drought stress. The similar chromosomal region on 4 and 6 were found to harbor QTLs for canopy temperature and leaf drying under drought stress conditions. Thus, the identified large effect yield QTLs could be introgressed to develop rice lines with stable yields under varying natural drought stress predominant in TPEs.

Genetic mapping and legume synteny of aphid resistance in African cowpea (Vigna unguiculata L. Walp.) grown in California

Abstract: The cowpea aphid Aphis craccivora Koch (CPA) is a destructive insect pest of cowpea, a staple legume crop in Sub-Saharan Africa and other semiarid warm tropics and subtropics. In California, CPA causes damage on all local cultivars from early vegetative to pod development growth stages. Sources of CPA resistance are available in African cowpea germplasm. However, their utilization in breeding is limited by the lack of information on inheritance, genomic location and marker linkage associations of the resistance determinants. In the research reported here, a recombinant inbred line (RIL) population derived from a cross between a susceptible California blackeye cultivar (CB27) and a resistant African breeding line (IT97K-556-6) was genotyped with 1,536 SNP markers. The RILs and parents were phenotyped for CPA resistance using field-based screenings during two main crop seasons in a 'hotspot' location for this pest within the primary growing region of the Central Valley of California. One minor and one major quantitative trait locus (QTL) were consistently mapped on linkage groups 1 and 7, respectively, both with favorable alleles contributed from IT97K-556-6. The major QTL appeared dominant based on a validation test in a related F2 population. SNP markers flanking each QTL were positioned in physical contigs carrying genes involved in plant defense based on synteny with related legumes. These markers could be used to introgress resistance alleles from IT97K-556-6 into susceptible local blackeye varieties by backcrossing.

Characterisation of 4274 accessions of common bean (Phaseolus vulgaris L.) germplasm conserved in the Indian gene bank for phenological, morphological and agricultural traits

Abstract: Common bean is one of the most important legume crops worldwide. Response to selection and success of hybridisation in common bean primarily depends on the nature and magnitude of genetic diversity present in the germplasm used. Germplasm comprising 4274 accessions originating from 58 countries were characterized for 22 phenotypic traits for two years. Genetic diversity for traits such as leaf length (4.5–20.7 cm), leaf width (3.4–17.5 cm), pod length (PL) (3.5–23.5 cm), no of pods/plant (4.2–59.6), seeds/pod (2.1–9.6) and 100-seed weight (SWT) (3.5–96.3 g) was observed in the accessions. Based on multivariate analysis, the entire collection was grouped into 10 genetically diverse clusters irrespective of the origin or place of collection of accessions. First three components obtained through principal component analysis explained 80.44 % of the total variance and it was contributed mainly by PL, pod width (PW), seed length (SL), seed width (SW), pods/plant and SWT. Correlation coefficient of seed weight was positively significant with leaf length, PL, PW, SL and SW while it was negatively correlated with days to flowering, pods/plant and seeds/pod. Regression analysis showed highest direct effect of SW on seed weight followed by SL, and PL. For bean anthracnose, >600 accessions showed resistance under field conditions, however when subjected to screening under artificial conditions against four most prevalent races (03, 515, 598 and 529) of Colletotrichum lindemutianum, we identified 16 accessions which have complete resistance and good agronomic superiority. These accessions may serve as useful genetic material to plant breeders for breeding bean varieties for anthracnose resistance and high yield.

Potato genetics, genomics, and applications

Abstract: Potato has a variety of reproductive uniquenesses besides its clonal propagation by tubers. These traits are controlled by a different kind of genetic control. The reproductive information has been applied to enable interspecific hybridization to enhance valuable traits, such as disease and pest resistances, from the tuber-bearing Solanum gene pool. While progress has been made in potato breeding, many resources have been invested due to the requirements of large populations and long time frame. This is not only due to the general pitfalls in plant breeding, but also due to the complexity of polyploid genetics. Tetraploid genetics is the most prominent aspect associated with potato breeding. Genetic maps and markers have contributed to potato breeding, and genome information further elucidates questions in potato evolution and supports comprehensive potato breeding. Challenges yet remain on recognizing intellectual property rights to breeding and germplasm, and also on regulatory aspects to incorporate modern biotechnology for increasing genetic variation in potato breeding.

Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping.

Abstract: Early vigour of rice, defined as seedling capacity to accumulate shoot dry weight (SDW) rapidly, is a complex trait. It depends on a genotype propensity to assimilate, store, and/or use non-structural carbohydrates (NSC) for producing large and/or numerous leaves, involving physiological trade-offs in the expression of component traits and, possibly, physiological and genetic linkages. This study explores a plant-model-assisted phenotyping approach to dissect the genetic architecture of rice early vigour, applying the Genome Wide Association Study (GWAS) to morphological and NSC measurements, as well as fitted parameters for the functional-structural plant model, Ecomeristem. Leaf size, number, SDW, and source-leaf NSC concentration were measured on a panel of 123 japonica accessions. The data were used to estimate Ecomeristem genotypic parameters driving organ appearance rate, size, and carbon dynamics. GWAS was performed based on 12 221 single-nucleotide polymorphisms (SNP). Twenty-three associations were detected at P <1×10(-4) and 64 at P <5×10(-4). Associations for NSC and model parameters revealed new regions related to early vigour that had greater significance than morphological traits, providing additional information on the genetic control of early vigour. Plant model parameters were used to characterize physiological and genetic trade-offs among component traits. Twelve associations were related to loci for cloned genes, with nine related to organogenesis, plant height, cell size or cell number. The potential use of these associations as markers for breeding is discussed.

TOND1 confers tolerance to nitrogen deficiency in rice

Abstract: Nitrogen (N), the most important mineral nutrient for plants, is critical to agricultural production systems. N deficiency severely affects rice growth and decreases rice yields. However, excessive use of N fertilizer has caused severe pollution to agricultural and ecological environments. The necessity of breeding of crops that require lower input of N fertilizer has been recognized. Here we identified a major quantitative trait locus on chromosome 12, Tolerance Of Nitrogen Deficiency 1 (TOND1), that confers tolerance to N deficiency in the indica cultivar Teqing. Sequence verification of 75 indica and 75 japonica cultivars from 18 countries and regions demonstrated that only 27.3% of cultivars (41 indica cultivars) contain TOND1, whereas 72.7% of cultivars, including the remaining 34 indica cultivars and all 75 japonica cultivars, do not harbor the TOND1 allele. Over-expression of TOND1 increased the tolerance to N deficiency in the TOND1-deficient rice cultivars. The identification of TOND1 provides a molecular basis for breeding rice varieties with improved grain yield despite decreased input of N fertilizers.

QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

Abstract: Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate rapid introgression of waterlogging tolerance in tropical maize breeding programs.

Characterization of a novel reduced height gene (Rht23) regulating panicle morphology and plant architecture in bread wheat

Abstract: Plant height and spikelet density are important agronomic traits related to plant architecture and grain yield in wheat. The development of wheat mutants not only provided new genetic resources for wheat improvement, but also facilitated our understanding of the regulation of these traits at the molecular level. Here, we report the identification of a dwarf mutant with a compact spike. NAUH164, produced from ethyl methyl sulfonate treatment of wheat variety Sumai 3, has reduced plant height and shortened spike length. Microscopic observations showed that the mutant has an atypical vascular bundle arrangement and overall smaller cell volumes. Sensitivity of seedlings to exogenous gibberellin was not changed, and plant height was not restored to the level of the wildtype. Dwarfness and compact spike were controlled by a single dominant gene that was designated Rht23, which was mapped 4.7 cM distal to SSR marker Gdm63 and 11.1 cM proximal to Barc110 on chromosome 5DL. Comparative sequence analysis of the co-linear regions in common wheat and Aegilops taushii indicated that Rht23 occurs in a physical interval of 8.5 Mb.

Conventional Plant Breeding Principles and Techniques

Abstract: Conventional plant breeding is the development or improvement of cultivars using conservative tools for manipulating plant genome within the natural genetic boundaries of the species. Mendel's work in genetics ushered in the scientific age of plant breeding. The number of genes that control the trait of interest is important to breeders. Qualitative traits (controlled by one or a few genes) are easier to breed than quantitative traits (controlled by numerous genes). General steps in breeding are: objectives, creation/assembly of variability, selection, evaluation and cultivar release. Breeders use methods and techniques that are based on the mode of reproduction of the species self-pollinating, cross-pollinating, or clonally propagated. The general strategy is to breed a cultivar whose genetic purity and productivity can be sustained by its natural mating system. There are six basic types of cultivars: pure line, open-pollinated, hybrid, clonal, apomictic and multilines. The common methods for breeding self-pollinated species include mass selection, pure line selection, pedigree, bulk population, single seed descent, backcrossing, multiline and composite. Methods for breeding cross-pollinated species include mass selection, recurrent selection, family selection and synthetics. Hybrid cultivar breeding exploits the phenomenon of heterosis, and is applicable to both self- and cross-pollinated species. Polyploids have complex genetics. Hybridization of parents is often accompanied by infertility of the hybrid. Mutation breeding may be resorted to when the gene of interest is non-existent in nature and may be induced. Also, sometimes, the desired trait is found in wild relatives of the species and may be introgressed into cultivated species through pre-breeding.

Characterization of a Triticum aestivum-Dasypyrum villosum T2VS·2DL translocation line expressing a longer spike and more kernels traits.

Abstract: By using 2V-specific EST–PCR markers and sequential GISH/FISH analysis, we identified four homozygous CS–2V translocation lines, including a novel compensating T2VS·2DL translocation line NAU422. This translocation line has longer spikes and produces more grains per spike than its recurrent parent CS and three other translocation lines, which could be a valuable resource in wheat yield improvement. Dasypyrum villosum (2n = 14, VV), the wild relative of wheat, possesses novel and superior alleles at many important loci and should be utilized to improve the genetic diversity of cultivated wheat and may be very helpful for the improvement of wheat yield. In this study, four homozygous Chinese Spring (CS)–D. villosum translocation lines containing different fragments of chromosome 2V were characterized from a pool, including 76 translocations that occur in chromosomes 1 V through 7 V of D. villosum by both molecular markers and cytogenetic analysis. A rough physical map of 2V was developed which included nine markers in three segments of the short arm and ten markers in the long arm. The photoperiod response gene of D. villosum (Ppd-V1) was physically mapped to the FL 0.33–0.53 region of 2VS, while the gene controlling bristles on the glume ridges (Bgr-V1) was mapped to 2VS FL 0.00–0.33. A novel compensating Triticum aestivum–D. villosum Robertsonian translocation line T2VS·2DL (NAU422) with good plant vigor and full fertility was further characterized by sequential genomic in situ hybridization and fluorescent in situ hybridization and the use of molecular markers. Compared to its recurrent parent CS and three other translocation lines, the T2VS·2DL translocation line has longer spikes, more spikelets and more grains per spike in two season years, which suggested that the alien segment may carry yield-related genes of D. villosum. The developed T2VS·2DL translocation line with its morphological and co-dominant molecular markers could be utilized as a novel germplasm for high-yield wheat breeding.

Legume Seed Production Meeting Market Requirements and Economic Impacts

Abstract: The seed is the carrier of the genetic improvements brought about by modern plant breeding, and seed production is carried out in accordance with certification systems to guarantee consistent high quality. In forage legumes, breeding efforts are primarily related to the vegetative development of the plant, although the commercial success of an agronomically superior cultivar is dependent on a reliable supply of competitively priced seed. In seed production of the three most important forage legumes, alfalfa (Medicago sativa L.), white clover (Trifolium repens L.), and red clover (Trifolium pratense L.), crop management techniques are applied to stimulate reproductive development in order to obtain high seed yields. These include a low plant density, manipulation of canopy size to avoid lodging and shading of fruiting organs, synchronization of flowering with pollinating insects as well as controlling pests. High seed yield is correlated to inflorescence density and seed yield per inflorescence, traits whi...

Plant Breeding in the Omics Era

Abstract: Contents 1. Introduction to Plant Breeding Plant Breeding and Society Genetics, Omics and Plant Breeding Populations Genetic Diversity Distances Measures Grouping Germplasm Quantitative Variation Mapping Traits Genotype-by-Environment Interaction Phenotyping Phenomics References 2. Plant Genetic Resources for Food and Agriculture Crop Evolution and Plant Species Feeding the World Genebanks Gene Pools Describing Variation and Identifying Redundancy Germplasm Evaluation Descriptors Documentation and Bioinformatics Geo-documentation to Identify Germplasm Genebank Sampling and Core Subsets Genomics of Plant Genetic Resources Putting Genes into Usable Forms References 3. Inbred Development DNA markers for Mapping Quantitative Trait Loci (QTL) and Aided Breeding Inbreeding and Line Development Doubled Haploids Adaptability: Learning for Model Plant Systems Breeding for Stress-prone Environments and Resource-use Efficiency Host-plant Resistance Breeding Participatory and Client-driven Plant Breeding References 4. Population Improvement Recurrent Selection and Breeding Populations Genome-wide Association and Quantitative Trait Variation Plant Genomics and Marker-assisted Selection Genomic Selection and Prediction of Breeding Values References 5. Heterosis and Inter-Specific Hybridization Heterotic Groups Hybrid Vigor Heterosis in Plant Breeding Understanding Hybrid Vigor in Model Plants and Crops Omics Research on Heterosis Hybrids in Selfing Species Polyploid Heterosis Interspecific hybridization References 6. Mutations and Epigenetics Induced Mutations and Plant Breeding Induced Mutations and Genomics-led Plant Breeding Targeting Induced Local Lesions IN Genomes (TILLING) Epigenetics References 7. Genetic Engineering and Transgenic Breeding Plant Genetic Engineering "Issues" Transgenic Crops "Risks" Transgene Flow Pest Resistance and Impacts on Non-target Organisms Detecting Genetically Modified Organisms and Other Safety Assessments Transgenic Agriculture and Co-existence Plant Genetic Engineering Impacts Transgenic Agriculture Outlook New Plant Breeding Techniques References 8. DNA Sequencing, other Omics and Synthetic Biology DNA Sequencing Next Generation Sequencing Genotyping-by-Sequencing Other Relevant Omics for Plant Breeding Breeding Informatics Case Study: Omics-led Legume Breeding Pl ant Synthetic Biology: Another Tool for Plant Breeding? References 9. Breeding Self-fertilizing Plants: From Inbred to Hybrid Cultivars Rice Domestication Genetic Enhancement Genomics Marker-aided Selection (MAS) Stress Breeding Interspecific Hybridization and Participatory Breeding Hybrid Cultivars Phenotyping Genetic Engineering Wheat Evolution and Diversity Germplasm Enhancement Resynthesizing Wheat Shuttle Breeding and Mega-environments Grain Yield Potential Perennial Wheat Biotechnology Ex ante and in silico Breeding Tomato References 10. Breeding Open Pollinated, Hybrid and Transgenic Outcrossing Species Maize Domestication and Diversity Germplasm Enhancement Breeding Inbred Line Development and Hybrids Doubled Haploids Genomics-led Improvement for Enhancing Genetic Gains Developing Stress-resilient Germplasm Nutritious Maize Prediction of Breeding Values Genetic Engineering Cotton Cassava Case Study: Cassava Breeding in sub-Saharan Africa References 11. Polyploidy and Plant Breeding Potato Origin, Diversity and Taxonomy Ploidy Manipulations Genetic Resources and Breeding True Potato Seed Genomics Genetic Engineering Banana/Plantain References 12. Seeds, Clones and Perennials Seed Development: Learning from a Model Plant System Inbred and Open Pollinated Seed Cultivars Hybrid Seed Rapid Multiplication of Healthy and Improved Planting Material of Vegetatively Propagated Crops Seed Health Apomixis: Procreation without Recreation Perennial Crops References 13. Diversity, Intellectual Property and Plant Variety Protection Plant Genetic Resources The Question of Derivatives Multinational Private and Public Seed Sectors Managing Agro-biotechnology Intellectual Property Rights References

Vavilovian Centers of Plant Diversity: Implications and Impacts

Abstract: N.I. Vavilov, Academician of the V.I. Lenin All-Union Academy of Agricultural Sciences, takes his place as a founding pillar of knowledge in the cathedral of the origin and development of cultivated plants. Relying on the theories of his revered predecessors, Charles Darwin and Alphonse de Candolle, Vavilov developed the concept of centers of origin for agronomic crops. Vavilov’s astute hypotheses set the stage for the modern use of exotic germplasm in plant breeding. Vavilov, a devoted scientist, continued to revise and refine his theory of the centers of origin throughout his lifetime based on additional plant collections and data evaluation. Though he initially proposed three in 1924, and eight in 1935, his final papers of 1940, discussed seven major centers with some minor additions. His concept of specific centers of origin for crop plants was not an isolated aphorism but has directed breeders, on their study and reflection, to the continued improvement and economic development of plants for humanity. Inherent genetic plant variability is the basis of domestication and breeding into crops of economic importance with food, fuel, fiber, and industrial uses. The objective of this article is to present a summary of Vavilov’s plant explorations. His collection trips led to the development of his theory of the centers of origin of cultivated crops, the law of homologous variation, as well as his concept of genetic erosion. Further modification of his theories by other scientists and the impact of his ideas are mentioned. His influence on present day conservation of genetic resources are presented.

DNA Marker Technologies in Plants and Applications for Crop Improvements

Abstract: Over the past several decades, especially through traditional breeding programme, intensive attempts have been made for the improvement of a large number of cereal varieties which adjusted to diverse agro-ecologies. However, increasing biotic and abiotic stresses, increasing populations, and sharply reducing natural resources especially water for agricultural purposes, push the breeders for organizing and developing improved cereal varieties with higher yield potential. In combination with developments in agricultural technology, plant breeding has made remarkable progress in increasing crop yields for over a century. Molecular markers are widely employed in plant breeding. DNA markers are being used for the acceleration of plant selection through marker-assisted selection (MAS). Genes of agronomic and scientific importance can be isolated especially on the basis of their position on the genetic map by using molecular markers technologies. In this review, the current status of marker development technologies for crop improvements will be discussed. It will also provide an outlook into the future approaches and most widely used applications in plant breeding in crop plants on the basis of present development.

Stability and genetic control of morphological, biomass and biofuel traits under temperate maritime and continental conditions in sweet sorghum (Sorghum bicolour).

Abstract: Eight morphological, biomass and biofuel traits were found with high broad-sense heritability and 18 significant QTLs discovered including one locus controlling the stem juice trait for sorghum grown in Denmark and China. Sweet sorghum with tall plant, fast maturation and high stem Brix content can be bred as a biofuel crop for Northern Europe. Sweet sorghum (Sorghum bicolour), a native tropical C4 crop, has attracted interest as a bioenergy crop in northern countries due to its juice-rich stem and high biomass production. Little is known about the traits important for its adaptation to high altitude climatic conditions and their genetic controls. Recombinant inbred lines derived from a cross between a sweet and a grain kaoliang sorghum were used in five field trials in Denmark and in China to identify the stability and genetic controls of morphological, biomass and biofuel traits during three consecutive summers with short duration, cool temperatures and long days. Eight out of 15 traits were found with high broad-sense heritability. Strong positive correlations between plant height and biomass traits were observed, while Brix and juice content were under different genetic controls. Using newly developed PAV (presence and absence variant) markers, 53 QTLs were detected, of which 18 were common for both countries, including a locus controlling stem juice (LOD score = 20.5, r 2 = 37.5 %). In Denmark, the heading stage correlated significantly with biomass and morphology traits, and two significant maturity QTLs detected on chromosomes SBI01 and SBI02 co-localised with QTLs previously associated with early-stage chilling tolerance, suggesting that accelerating maturation might be a means of coping with low-temperature stress. Our results suggest that selection for tall and fast maturating sorghum plants combined with high Brix content represents a high potential for breeding bioenergy crop for Northern Europe.

Genetic evidence for differential selection of grain and embryo weight during wheat evolution under domestication

Abstract: Wheat is one of the Neolithic founder crops domesticated ~10 500 years ago. Following the domestication episode, its evolution under domestication has resulted in various genetic modifications. Grain weight, embryo weight, and the interaction between those factors were examined among domesticated durum wheat and its direct progenitor, wild emmer wheat. Experimental data show that grain weight has increased over the course of wheat evolution without any parallel change in embryo weight, resulting in a significantly reduced (30%) embryo weight/grain weight ratio in domesticated wheat. The genetic factors associated with these modifications were further investigated using a population of recombinant inbred substitution lines that segregated for chromosome 2A. A cluster of loci affecting grain weight and shape was identified on the long arm of chromosome 2AL. Interestingly, a novel locus controlling embryo weight was mapped on chromosome 2AS, on which the wild emmer allele promotes heavier embryos and greater seedling vigour. To the best of our knowledge, this is the first report of a QTL for embryo weight in wheat. The results suggest a differential selection of grain and embryo weight during the evolution of domesticated wheat. It is argued that conscious selection by early farmers favouring larger grains and smaller embryos appears to have resulted in a significant change in endosperm weight/embryo weight ratio in the domesticated wheat. Exposing the genetic factors associated with endosperm and embryo size improves our understanding of the evolutionary dynamics of wheat under domestication and is likely to be useful for future wheat-breeding efforts.

Improving the phenotypic expression of rice genotypes: Rethinking “intensification” for production systems and selection practices for rice breeding

Abstract: Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and (initially) more labor, as seen from the System of Rice Intensification (SRI), whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However, unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the expression of rice plants' genetic potential, thereby creating more productive and robust phenotypes from given rice genotypes. Data indicate that increased plant density does not necessarily enhance crop yield potential, as classical breeding methods suggest. Developing cultivars that can achieve their higher productivity under a wide range of plant densities—breeding for density-neutral cultivars using alternative selection strategies—will enable more effective exploitation of available crop growth resources. Density-neutral cultivars that achieve high productivity under ample environmental growth resources can also achieve optimal productivity under limited resources, where lower densities can avert crop failure due to overcrowding. This will become more important to the extent that climatic and other factors become more adverse to crop production. Focusing more on which management practices can evoke the most productive and robust phenotypes from given genotypes is important for rice breeding and improvement programs since it is phenotypes that feed our human populations.

Genetic Divergence and Heritability of 42 Coloured Upland Rice Genotypes (Oryzasativa) as Revealed by Microsatellites Marker and Agro-Morphological Traits.

Abstract: Coloured rice genotypes have greater nutritious value and consumer demand for these varieties is now greater than ever. The documentation of these genotypes is important for the improvement of the rice plant. In this study, 42 coloured rice genotypes were selected for determination of their genetic divergence using 25 simple sequence repeat (SSR) primers and 15 agro-morphological traits. Twenty-one out of the 25 SSR primers showed distinct, reproducible polymorphism. A dendrogram constructed using the SSR primers clustered the 42 coloured rice genotypes into 7 groups. Further, principle component analysis showed 75.28% of total variations were explained by the first-three components. All agro-morphological traits showed significant difference at the (p≤0.05) and (p≤0.01) levels. From the dendrogram constructed using the agro-morphological traits, all the genotypes were clustered into four distinct groups. Pearson's correlation coefficient showed that among the 15 agro-morphological traits, the yield contributing factor had positive correlation with the number of tillers, number of panicles, and panicle length. The heritability of the 15 traits ranged from 17.68 to 99.69%. Yield per plant and harvest index showed the highest value for both heritability and genetic advance. The information on the molecular and agro-morphological traits can be used in rice breeding programmes to improve nutritional value and produce higher yields.