Showing papers in "Euphytica in 2014"

Flowering time in wheat (Triticum aestivum L.): a key factor for global adaptability

Abstract: Wheat is one of the most widely cultivated crops and, being the staple diet of more than 40 countries, it plays an imperative role in food security. Wheat has remarkable genetic potential to synchronize its flowering time with favourable environmental conditions. This ability to time its flowering is a key factor for its global adaptability and enables wheat plant to produce satisfactory grain yield under very diverse temperature and soil moisture conditions. Vernalization (Vrn), photoperiod (Ppd) and earliness per se (Eps) are the three genetic systems controlling flowering time in wheat. The objective of this review is to provide comprehensive information on the physiological, molecular and biological aspects of the three genetic constituents of flowering and maturity time in wheat. Reviews written in the past have covered either one of the aspects; and generally focused on one of the three genetic constituents of the flowering time. The current review provides (a) a detailed overview of all three gene systems (vernalization, photoperiod and earliness per se) controlling flowering time, (b) details of the primer sequences, their annealing temperatures and expected amplicon sizes for all known markers of detecting vernalization and photoperiod alleles, and (c) an up to date list of QTLs affecting flowering and/or maturity time in wheat.

Current knowledge on Amaranthus spp.: research avenues for improved nutritional value and yield in leafy amaranths in sub-Saharan Africa

Abstract: In the past 20 years, very little progress has been achieved in reducing food insecurity, child malnutrition and hunger in Africa. Under-nutrition and micronutrients deficiencies are widespread and affect mainly women and children. To address these problems, increased consumption of African leafy vegetables is promoted as sources of both micronutrients and bio-active compounds. Widely promoted African leafy vegetables include Amaranthus spp., a taxonomic group cultivated worldwide. Species of this genus are used as pseudo-cereals in Europe and America, and are mostly planted as vegetables in Africa. Amaranthus has been rediscovered as a promising food crop mainly due to its resistance to heat, drought, diseases and pests, and the high nutritional value of both seeds and leaves. Leaves are rich in proteins and micronutrients such as iron, calcium, zinc, vitamin C and vitamin A. All parts of the plant are used as medicine to heal many diseases in African communities. This paper focuses on leafy amaranths traditionally utilized on the continent. It briefly reviews the current knowledge on taxonomy, ecology, nutritional and nutraceutical value, production and cultivation systems, reproductive biology, genetic resources and breeding of amaranths. Species of interest include: A. blitum, A. caudatus, A. cruentus, A. dubius, A. hypochondriacus, A. spinosus, A. thunbergii, A. tricolor, and A. viridis. Research and development opportunities on nutritive and nutraceutical properties, production and commercialization, taxonomic evaluation and breeding perspectives were explored.

Utilization of crop heterosis: a review

Abstract: Heterosis (or hybrid vigor) is a natural phenomenon whereby hybrid offspring of genetically diverse individuals display improved physical and functional characteristics relative to their parents. Heterosis has been increasingly applied in crop production for nearly a century, with the aim of developing more vigorous, higher yielding and better performing cultivars. In this review we present and compare three categories of crop heterosis utilization: intraspecific heterosis, intersubspecific heterosis and wide-hybridization heterosis, with particular focus on polyploid species. Different pollination-control systems used to breed for heterosis are also comparatively analyzed. Finally, we highlight problems involved in heterosis research and crop improvement. We aim to provide insight into best practices for amplifying heterosis potential.

Introgression genetics and breeding between Upland and Pima cotton: a review

Abstract: The narrow genetic base of elite Upland cotton (Gossypium hirsutum L.) germplasm has been a significant impediment to sustained progress in the development of cotton cultivars to meet the needs of growers and industry in recent years. The prospect of widening the genetic base of Upland cotton by accessing the genetic diversity and fiber quality of Pima cotton (Gossypium barbadense L.) has encouraged interspecific hybridization and introgression efforts for the past century. However, success is limited due mainly to genetic barriers between the two species in the forms of divergent gene regulatory systems, accumulated gene mutations, gene order rearrangements and cryptic chromosomal structure differences that have resulted in hybrid breakdown, hybrid sterility and selective elimination of genes. The objective of this paper is to provide a mini-review in interspecific hybridization between Upland and Pima cotton relevant to breeding under the following sections: (1) qualitative genetics; (2) cytogenetic stocks; (3) quantitative genetics; (4) heterosis, and (5) introgression breeding. Case studies of successful examples are provided.

Genetic progress in wheat yield and associated traits in China since 1945 and future prospects

Abstract: Genetic progress has brought about a dramatic increase in yield potential per se for almost all production areas around the world. The present study examines the relationship of wheat yield with year of release, yield components, harvest index (HI), biomass production, and plant height. We used aggregative data from 1945 to 2010 to calculate genetic gain in wheat yield across different zones in China. A deeper understanding of these issues facilitates the identification of specific yield-limiting factors that can be used for future breeding strategies. Absolute yield gain for the different zones was found to range from 20 to 103 kg ha−1 year−1, whereas relative yield gain ranged from 0.33 to 1.42 % per year. When data from all the Chinese wheat production zones was pooled, yield gain at the national level had an absolute value of 66 kg ha−1 year−1 and a relative value of 1 % per year. Grain weight and spike weight, rather than the other yield components, are significantly correlated with year of release for most zones, suggesting that these two were the most promising traits for breeders in the past. These two traits are also responsible for the significant genetic progress in wheat yield in China since 1949. HI and biomass production also showed strong correlation with year of release and grain yield. In China, HI and grain weight have experienced such a substantial increase that both have almost reached their theoretical maxima in the period 1945–2010. Further improvement in the yield potential of wheat will have to involve increase in biomass production and grain number. This paper also reviews cropping systems and technologies as well as improvement in physiological trait from 1945 onwards during the period of genetic gain.

QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping

Abstract: Direct seeding is becoming more popular mainly due to its labor-saving nature. However, flooding during germination caused by unleveled fields and unpredicted heavy rain can prevent crop establishment. On the other hand, flooding just after sowing protects the seeds from rats and birds and is also a viable means of weed control. Thus, the development of varieties able to tolerate flooding during germination, referred to as anaerobic germination (AG), is essential. A study was conducted to identify QTLs associated with tolerance of flooding during germination from an F2:3 mapping population derived from the cross of IR64 and the tolerant aus landrace Nanhi. Phenotyping was performed by counting the rate of seedling survival of 300 lines under the stress. Selective genotyping was employed by genotyping the 48 most tolerant and 48 most susceptible lines using a 384-plex SNP Indica/Indica set on the Illumina BeadXpress Reader, resulting in 234 polymorphic markers for the study. A major QTL for AG derived from Nanhi, named qAG7, was detected on chromosome 7 with an LOD of 13.93 and 22.3 % of the phenotypic variance explained. A second QTL of smaller effect, qAG11, was also derived from Nanhi, while one QTL with an increased effect from IR64 was detected on chromosome 2 (qAG2.1). The QTLs detected in this study can be used to further elucidate the mechanisms underlying AG tolerance in rice, and can also be used in marker-assisted selection and QTL pyramiding to provide higher AG tolerance to enable improved crop establishment in direct-seeded systems.

Detection of downy and powdery mildew resistance QTL in a ‘Regent’ × ‘RedGlobe’ population

Abstract: One hundred and eighty six F1 plants from a ‘Regent’ × ‘RedGlobe’ cross were used to generate a partial linkage map with 139 microsatellite markers spanning all 19 chromosomes. Phenotypic scores for downy mildew, taken over two years, confirmed a major resistance QTL (Rpv3) against downy mildew in the interval VVIN16-cjvh to UDV108 on chromosome 18 of ‘Regent’. This locus explained up to 62 % of the phenotypic variance observed. Additionally a putative minor downy mildew resistance locus was observed on chromosome 1 in one season. A major resistance locus against powdery mildew (Ren3) was also identified on chromosome 15 of ‘Regent’ in the interval UDV116 to VChr15CenGen06. This study established the efficacy of and validated the ‘Regent’-derived downy and powdery mildew major resistance genes/QTL under South African conditions. Closely linked SSR markers for marker-assisted selection and gene pyramiding strategies were identified.

Molecular tagging of QTLs for fiber quality and yield in the upland cotton cultivar Acala-Prema

Abstract: Cotton is a high-value per acre crop that is produced as a raw material for the textile industry. With the development of new technologies in the textile industry, much attention has been paid to fiber quality in conjunction with yield. The introgression cultivar “Acala Prema” is extensively planted in the Carolina/USA for its good fiber qualities, high yields and tolerance to Verticillium wilt. To conduct QTL mapping for fiber quality and yield in Acala-Prema, we developed a population of 180 recombinant inbred lines (RILs) from a single seed derived from a cross between this line and Chinese cultivar 86-1. We examined the yield performance of the RILs in five Chinese environments and fiber qualities in seven Chinese environments. A genetic linkage map comprising 279 loci was constructed using this RIL population, chiefly with SSR markers, and QTLs were repeatedly identified across diverse environments using the composite interval mapping method. A total of 86 nonredundant QTLs for yield and its components and fiber qualities were independently detected in five or seven environments; Prema alleles were responsible for the increase in trait values for 46 QTLs, while 86-1 was responsible for 40 QTLs. Notably, we detected the stable fiber strength QTL qFS-D3-1, which explained 4.51–17.55 % of PV, with LOD scores ranging from 2.83 to 7.09, and the fiber length qFL-D11-1, which explained 10.02–25.34 % of the PV. Eighteen environment epistatic QTLs were also detected. The QTLs detected in this study provide new information for improving fiber quality and may be especially valuable for marker-assisted selection.

Stripe rust resistance and genes in Chinese wheat cultivars and breeding lines

Abstract: Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases on wheat in China. To assess resistance in wheat cultivars and breeding lines in China, 330 leading cultivars and 164 advanced breeding lines were evaluated with stripe rust. In the greenhouse tests, seedlings of the entries were inoculated separately with several Pst pathotypes. In the field tests, the entries were evaluated for stripe rust resistance in Yangling, Shaanxi Province artificially inoculated and in Tianshui, Gansu Province under natural infection of Pst. The oversummering/wintering and spring epidemic zones of resistance genes were postulated using molecular markers for Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, and Yr26, in combination with resistance spectra. Out of the 494 wheat entries, 16 (3.24 %) entries had all-stage resistance (ASR) in all race tests, 99 (20.04 %) had adult-plant resistance (APR), 28 (5.67 %) were considered to have slow-rusting (SR), and 351 (71.05 %) were susceptible to one or more races in both seedling and adult-plant stages. Advanced breeding lines had a higher percentage (37.2 %) of resistant entries (The sum of ASR, APR and SR) than leading cultivars (24.85 %). Among the epidemic regions, southern Gansu had a higher percentage of resistant entries than any other regions. Based on stripe rust reactions and molecular markers, two cultivars were found to possibly have Yr5 while no entries have Yr10 or Yr15. Resistance genes Yr9, Yr17, Yr18, and Yr26 were found in 134 (29.4 %), 45 (9.1 %), 10 (2 %), and 15 (3 %) entries, respectively.

Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm ( Oryza sativa L.) with PCR based makers

Abstract: Molecular screening and genetic diversity of major rice blast resistance (R) genes were determined in 32 accessions of rice germplasm from North East and Eastern India with ten gene based single nucleotide polymorphisms and sequence tagged sites (STS) markers, namely z56592, zt56591, k39512, k3957, candidate gene marker, Pita3, YL155/YL87, YL183/YL87, Pb28, 195R-1 which showed close-set linkage to nine major rice blast resistance (R) genes, Piz, Piz-t, Pik, Pik-p, Pik-h, Pita/Pita-2, Pib and Pi9 and one susceptible pita gene. Among the 32 accessions, 13 were positive for Piz gene and six for Piz-t gene. Six accessions were positive for Pik gene, seven for Pik-p and 16 for Pik-h gene. One accession, Atte thima, was positive for three of Pik multiple genes. Out of 32, only two germplasm, Dudhraj and Nepali dhan, were detected with both Pita3 and YL155/YL87 marker for Pita/Pita-2 gene. The Pib gene appeared to be omnipresent and was detected in 31 of 32 germplasm with marker Pb28. The gene specific STS marker, 195R-1, for Pi9 gene produced positive bands in only two germplasm, Kalchatti and Bachi thima. The Uniform Blast Nursery (UBN) analysis showed that out of 32, six germplasm was resistant, ten moderately resistant and 16 germplasm were susceptible. Presence of Piz-t, Pita/Pita-2 and Pi9 gene ensured a resistant reaction in outdoor blast nursery whereas germplasm carrying Pib was susceptible when present alone. Presence of multiple genes, however, contributed to slow blasting resistance in the field. These results are useful in identification and incorporation of resistant genes from the germplasm into elite cultivars through marker assisted selection in rice breeding programs.

Genetics and mapping of quantitative traits for nodule number, weight, and size in soybean ( Glycine max L.[Merr.])

Abstract: Soybean research has found that nodule traits, especially nodule biomass, are associated with N2 fixation ability. Two genotypes, differing in nodule number per plant and individual nodule weight, KS4895 and Jackson, were mated to create 17 F3- and 80 F5-derived RILs. The population was mapped with 664 informative markers with an average distance of less than 20 cM between adjacent markers. Nodule traits were evaluated in 3-year field trials. Broad-sense heritability for nodule number (no. plant−1), individual nodule dry weight (mg nodule−1), individual nodule size (mm nodule−1), and total nodule dry weight (g plant−1) was 0.41, 0.42, 0.45, and 0.27, respectively. Nodule number was negatively correlated with individual nodule weight and size. Nodule number, individual nodule weight, and size are major components which likely contributed to increased total nodule weight per plant. Composite interval mapping (CIM) identified eight QTLs for nodule number with R2 values ranging from 0.14 to 0.20. Multiple interval mapping (MIM) identified two QTLs for nodule number, one of which was located close to the QTL identified with CIM. Six QTLs for individual nodule weight were detected with CIM, and one QTL was identified with MIM. For nodule size, CIM identified seven QTLs with R2 values ranging from 0.14 to 0.27. Five QTLs for total nodule weight were detected with CIM, one of which was located close to a QTL identified with MIM. These results document the first QTL information on nodule traits in soybean from field experiments utilizing a dense, complete linkage map.

Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response

Abstract: Members of the APETALA2/ethylene response factor (AP2/ERF) transcription factor superfamily are widely present in plants and play important roles in the plant cell cycle, growth and development, as well as the response to biotic and abiotic stresses. The maize genome project has been completed; therefore, it is possible to identify all of the AP2/ERF genes in the maize genome. In this study, 184 AP2/ERF genes were identified by an in silico cloning method, and were compared with AP2/ERF genes from Arabidopsis, rice, grape and poplar. The 184 AP2/ERF maize genes were classified into four subfamilies: DREB (51), ERF (107), AP2 (22) and RAV (3), as well as one soloist. The amino acid sequence composition, physical and chemical characteristics, phylogenetic trees, conserved domain sequences, functional domains, and chromosomal location of the genes were predicted and analyzed. The 184 AP2/ERF genes are distributed on maize chromosomes 1–10 (31, 21, 13, 19, 22, 18, 21, 16, 11 and 12 genes, respectively). Under 0, 1, 2, 4 h waterlogging stress, the expression of 184 AP2/ERF genes in root of Hz32 inbred line (tolerance to waterlogging) were performed using RNA-sequence, and the result showed that 38 genes were responsive to waterlogging stress. This study lays the foundation for subsequent cloning and investigation of the function of the AP2/ERF genes responding to waterlogging stress in maize.

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

Abstract: Fifty-eight F2 individuals derived from an interspecific cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, were phenotyped for 42 plant, leaf, flower, and fruit traits. Composite interval mapping analysis using genotypic data from 736 molecular markers revealed the positions of 71 statistically significant (P ≤ 0.05) quantitative trait loci (QTL) influencing 32 of the morphological traits. Although most QTL were location-specific, QTL governing three traits (leaf lobing, leaf prickles and prickle anthocyanin) were detected in both experimental locations. Analysis of three additional traits (stem prickles, fruit calyx prickles and fruit length) in both locations yielded QTL in similar but non-overlapping map positions. The majority (69 %) of the QTL corresponded closely with those detected in previous analyses of this data set. However the increased resolution of the linkage map combined with advances in QTL mapping permitted more precise localization, such that the average interval length of these QTL was reduced by 93 %. Thirty-one percent of the QTL were novel, suggesting that simple linear regression with a low density linkage map (the method used in previous studies of this population) missed a substantial portion of significant QTL. Hotspots of QTL affecting plant hairiness, prickliness, and pigmentation were identified on chromosomes 3, 6, and 10, respectively, and may reflect the pleiotropic activity of single structural or regulatory genes at these positions. Based on synteny between the eggplant, tomato, potato and pepper genomes, putative orthologs were identified for 35 % of the QTL suggesting strong conservation of gene function within the Solanaceae. These results should make it easier to target particular loci for map-based cloning and marker-assisted selection studies.

Genetic combining ability and heterosis for important vitamins and antioxidant pigments in cauliflower ( Brassica oleracea var. botrytis L.)

Abstract: This study is the first report of combining ability and heterosis for important vitamins and antioxidant plant pigments in cauliflower. Five CMS lines were crossed with 8 male fertile lines in line × tester design to develop 40 hybrids. These hybrids along with parental lines were evaluated for different vitamins and anti-oxidant pigments to reveal extent of heterosis and genetic combining ability. The CMS line Ogu12A was good general combiner (gca effect) and Ogu16A was poor general combiner for most of the important traits under study. Most of the heterotic hybrid combinations were associated high specific combing ability (sca effect). However, gca effect was also important in developing quality heterotic hybrids. The proportions of $$\sigma_{\text{gca}}^{ 2} /\sigma_{\text{sca}}^{2}$$ were less than unity in all the cases indicating the role of non-additive gene action for most of the traits. Highest number of heterotic hybrids in positive direction was recorded for ascorbic acid content followed by anthocyanin content. The accumulated average heterosis of the 40 hybrids was in positive direction for ascorbic acid, anthocyanin and lycopene concentration whereas it was in negative direction for carotenoids and chlorophyll pigments. Very high heterosis for ascorbic acid, anthocyanin and carotenoids in cauliflower indicated the scope for development of F1 hybrids with higher concentration of these vitamins and anti-oxidant pigments. It is possible to develop heterotic hybrids for different vitamins and anti-oxidant plant pigments through selection of parental lines based on desirable genetic combing ability.

Diversity of crop development traits and nitrogen use efficiency among potato cultivars grown under contrasting nitrogen regimes

Abstract: Potato (Solanum tuberosum L.) requires abundant nitrogen (N) to perform well and has low nitrogen use efficiency (NUE). We assessed phenotypic variation among 189 potato cultivars for NUE and the association between NUE and ecophysiological variables describing canopy development (CDv), under high and low N input. In 2009 and 2010, 189 cultivars were grown with N supply (soil N + fertiliser N) of 75 or 180 kg N/ha at Bant, the Netherlands. CDv was assessed weekly as the percentage of soil covered by green potato leaves (%SC). Data were analysed using a model that described CDv as a function of thermal time, based on the Beta function and estimates of cardinal temperatures. Nitrogen significantly affected model-derived, biologically relevant, curve-fit parameters for each cultivar. The t 1 (i.e., thermal time required to reach maximum soil cover (Vx)) was higher at low than at high N. Other parameters were higher at high than at low N, especially Vx and the period over which it was maintained. Nitrogen also affected tuber dry matter yield, tuber size and weight distributions, N content and N uptake but not tuber dry matter percentage. The total area under the %SC curve was highly correlated with yield in both years. Cultivars performing well under high N also performed well under low N. There was large variation in NUE component traits among cultivars; maturity type partially explained this variation. Variables of the CDv model captured this variation, N effects on light interception and its correlation with yield.

Genetic analysis of drought tolerance in adapted × exotic crosses of maize inbred lines under managed stress conditions

Abstract: Introduced maize (Zea mays L.) germplasm can serve as sources of favorable alleles to enhance performance in new maize varieties and hybrids under drought stress conditions. In the present study, the combining abilities of 12 exotic maize inbred lines from CIMMYT and 12 adapted maize inbred lines from IITA were studied for grain yield and other traits under controlled drought stress. The inbred lines from each institution were separated into groups using SSR-based genetic diversity and were intercrossed using a factorial mating scheme to generate 96 hybrids. These hybrids were evaluated under both controlled drought stress and well-watered conditions at Ikenne in Nigeria in 2010 and 2011. Average mean yields of hybrids under drought stress represented 23 % of the average yield of hybrids under full irrigation. General combining ability (GCA) effects accounted for 49–85 % of the observed variation for several traits recorded under both well-watered and drought stress conditions. Specific combining ability effects for grain yield, though positive in most hybrids, were not significant under drought stress conditions. All the twelve exotic and nine adapted lines had positive GCA effects (female, male, or both) for grain yield under either drought stress or full irrigation, or both environments. EXL03 and EXL15 that had positive and significant female and male GCA effects for grain yield under both environments can be used to improve their adapted counterparts for grain yield and drought tolerance. Normalized difference vegetation index had weak but significant correlation with grain yield.

Development and characterization of genic SSR markers for mungbean (Vigna radiata (L.) Wilczek)

Abstract: Mungbean (Vigna radiata (L.) Wilczek) is an important food legume, but has limited genomic resources. In this study, the development of genic SSR markers from mungbean transcriptome sequences and their transferability to related Vigna species is presented. A total of 12,596 EST sequences from mungbean genotype ‘Jangan’ were searched for the presence of SSRs and 2,299 SSR motifs from 1,848 SSR containing unique ESTs were identified with an average of one SSR per 3.4 kb. Trinucleotide motifs (48 %) were the most abundant repeats followed by di- (25 %), tetra- (15 %), hexa- (7 %) and penta- (5 %) nucleotide repeats. Based on these SSR containing sequences, PCR primer pairs were successfully designed for 1,742 SSR loci and randomly selected 100 primer pairs were further used for characterization. Sequences analyses indicate that about 45 % of the SSR motifs were present in the coding sequences (CDS) and 55 % were located in the untranslated regions (UTRs). Trinucleotide repeats (62 %) were preferentially present in the CDS. Randomly selected 27 SSR markers were used to study the genetic relationship among 20 mungbean genotypes. Twenty one (78 %) genic SSR markers showed polymorphism and the number of alleles ranged from two to six with an average PIC value of 0.34. Cluster analysis based on similarity coefficient clearly separated the cultivated and the wild genotypes into separate groups. Transferability study showed that 97 % SSR markers were transferable to eight other Vigna species, hereby expanding their utility. This study gives an insight into frequency, type and distribution of SSRs in the genic region of mungbean and report the development of a large set of SSR markers for mungbean. These genic SSR markers will provide an important genomic resource for qualitative and quantitative traits mapping, marker assisted selection and genetic diversity studies in mungbean and related Vigna species.

A naturally occurring long insertion in the first intron in the Brassica rapa FLC2 gene causes delayed bolting

Abstract: We investigated the molecular basis of an extremely late bolting, non-heading ‘Leafy Green Parental Line No. 2 (Tsukena No. 2)’, to obtain suitable DNA markers for breeding the late bolting trait in Chinese cabbage (Brassica rapa L. ssp. pekinensis). We found that Tsukena No. 2 contains a ~5 kbp large insertion near the 5′ end of the first intron of BrFLC2, BrFLC3 and BrFLC3′, which are homologs of an Arabidopsis repressor gene for floral transition, FLOWERING LOCUS C (FLC). The transcript abundance of BrFLC1 in Tsukena No. 2 was repressed during cold exposure to the same level as found in a mid-season bolting commercial F1 variety “Muso” (heading Chinese cabbage) and an early-bolting parent of commercial F1 varieties, “Early” (Sakata Co.), whereas repression of BrFLC2 and BrFLC3 containing the large insertion was weak. Furthermore, QTL analysis of a F2 population derived from the Tsukena No. 2 × “Early” revealed that polymorphisms at the BrFLC2 and BrFLC3 loci explained 46.0 and 9.9 % of the phenotypic variation in the bolting time of vernalized plants, respectively. In Arabidopsis, cold-induced repression of FLC and maintenance of that repression are associated with the first intron of FLC. Our study suggests that a naturally occurring large insertion in the first intron resulted in weak repression of BrFLC2 and BrFLC3 during cold exposure and therefore explains the extremely late bolting of the Tsukena No. 2 cultivar.

Phenotypic diversity among local Spanish and foreign peach and nectarine [Prunus persica (L.) Batsch] accessions

Abstract: Phenotypic data for tree and fruit characteristics was collected over three consecutive years from a germplasm collection of 94 peach and nectarine accessions representing both traditional Spanish as well as foreign cultivars with widespread global plantings. All accessions were grown at the Experimental Station of Aula Dei located in the Ebro Valley (Northern Spain, Zaragoza) under a Mediterranean climate. Tree traits evaluated included bloom and harvest date, vigor, yield, yield efficiency and flower and leaf characteristics. Fruit traits included fresh weight, firmness, soluble solids, titratable acidity, levels of individual soluble sugars (sucrose, glucose, fructose and sorbitol), vitamin C, total phenolics, flavonoids, anthocyanins, relative antioxidant capacity and ripening index. Extensive variability was observed for most qualitative and quantitative traits with significant correlations identified between many traits. While the traditional Spanish accessions demonstrated good adaptability to the northern Spain evaluation site, opportunities for continued improvement in tree and fruit quality traits were demonstrated by an extensive phenotypic variability within the germplasm collection.

QTLs for barley yield adaptation to Mediterranean environments in the ‘Nure’ × ‘Tremois’ biparental population

Abstract: Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology®-based barley map has been developed in the ‘Nure’ × ‘Tremois’ biparental Doubled Haploid population, harbouring the genomic position of a gene set with a putative role in the regulation of flowering time and abiotic stress response in barley. The population has been evaluated in eighteen location-by-year combinations across the Mediterranean basin. QTL mapping identified several genomic regions responsible for barley adaptation to Mediterranean conditions in terms of phenology, grain yield and yield component traits. The most frequently detected yield QTL had the early flowering HvCEN_EPS2 locus (chromosome 2H) as peak marker, showing a positive effect from the early winter parent ‘Nure’ in eight field trials, and explaining up to 45.8 % of the observed variance for grain yield. The HvBM5A_VRN-H1 locus on chromosome 5H and the genomic region possibly corresponding to PPD-H2 on chromosome 1H were significantly associated to grain yield in five and three locations, respectively. Environment-specific QTLs for grain yield, and clusters of yield component QTLs not related to phenology and or developmental genes (e.g. on chromosome 4H, BIN_09) were observed as well. The results of this work provide a valuable source of knowledge and tools for both explaining the genetic bases of barley yield adaptation across the Mediterranean basin, and using QTL-associated markers for MAS pre-breeding and breeding programmes.

Identification of QTLs for cold tolerance at seedling stage in rice (Oryza sativa L.) using two distinct methods of cold treatment

Abstract: Cold water irrigation and growth in low temperature phytotron are two commonly used methods to evaluate cold tolerance of rice at the seedling stage and the cold sensitive seedlings exhibit different injury symptoms, respectively. However, so far no one has systematically dissected the differences of cold tolerance at seedling stage in rice under the two cold environments. We used a recombinant inbred line (RIL) population derived from a cross of a cold-tolerant japonica cultivar, Lijiangxintuanheigu and a cold sensitive indica cultivar, Sanhuangzhan-2 for this study. The cold sensitive seedlings exhibited leaf yellowing after cold water irrigation and leaf rolling during growth in the low temperature phytotron. Leaf yellowing and leaf rolling in RILs was significantly correlated, but the correlation coefficient was low. A total of four quantitative trait locus (QTLs) on chromosomes 1, 6, 9 and 12 were detected using leaf yellowing and percent seedling survival as indicators of cold tolerance after cold water irrigation, while five QTLs on chromosomes 7, 8, 9, 11 and 12 were detected using leaf rolling and percent seedling survival as indicators of cold tolerance during growth in the low temperature phytotron. The two QTLs, qCTS-9 and qCTS-12 were detected using different evaluation indicators under the two cold environments. Our results suggest that rice cold tolerance mechanisms at the seedling stage differ between the two environments, but the detection of common QTL implies the existence of overlap in the metabolic pathways for cold tolerance. The two common QTLs have potential value in rice breeding.

Identifying QTL for fiber quality traits with three upland cotton (Gossypium hirsutum L.) populations

Abstract: Cotton fiber quality was quantitative trait, controlled by multiple genes. Identification of stable quantitative trait loci (QTL) effectively contributing to favorable fiber quality traits would provide the key basis for marker-assisted selection used in molecular breeding projects. Three upland cotton F2 populations were established with a common parent Chinese cultivar Yumian 1 and three American commercial cultivars/lines (Acala Maxxa, CA3084 and TAM94L-25), each of which had unique fiber quality characteristic that was favorable economically. Three whole genome genetic maps were constructed with 323, 302 and 262 SSR loci for population (Yumian 1 × Acala Maxxa), (Yumian 1 × CA3084), and (Yumian 1 × TAM 94L-25) respectively, spanning 1,617.2, 1,639.9 and 1,441.4 cM. Based on these genetic maps and three generation phenotypic data of fiber quality traits (F2, F2:3 and F2:4), 77 QTL were detected, including 19 for fiber length, 14 for fiber uniformity, 17 for micronaire, 10 for fiber elongation, and 17 for fiber strength. Among these QTL, 46 QTL were significant QTL and 31 were putative QTL, including that one QTL (qFL05.1) and four QTL (qFL23.1, qFM06.1, qFM06.2 and qFE25.1) were detected across three and two populations respectively; two QTL qFL10.1 (Yumian 1 × TAM 94L-25) and qFL15.1 (Yumian 1 × Acala Maxxa) were detected in three generations; qFM23.1, qFE18.1 and qFS21.2 detected in population (Yumian 1 × CA3084), qFE10.1, and qFS10.2 detected in population (Yumian 1 × TAM 94L-25), and qFS15.1 detected in population (Yumian 1 × Acala Maxxa), were all detected in two generations. Alleles underlying these stable QTL were valuable candidate gene for fine mapping, cloning, and favorable gene pyramiding projects. Our study also verified that QTL mapping of fiber quality traits using multiple populations with a common parent had higher efficiency compared to single population crossed with two parents and favorable alleles contributed to QTL effect could be conferred by parents with inferior fiber quality traits.

Diversity evaluation of morphological traits and allicin content in garlic (Allium sativum L.) from China

Abstract: China has a long history in garlic cultivation and is the biggest country of garlic production in the world. 375 accessions of garlic from 23 provinces and areas in China has been collected and preserved in national germplasm repository for vegetatively propagated vegetables in Beijing since 2002. However, the genetic background and diversity of garlic from China has not been well characterized. In this study, 212 of 375 accessions of garlic were evaluated based on 29 morphological traits and allicin content. Cluster, principal compound, principal ordinates, Shannon diversity index and Pearson correlation analysis were used. The results showed that the garlic clones from China had a widely diversity among all traits. Principal component analysis showed the cumulative proportion of the first eight components explained 71.35 % of total morphological variation in all accessions. Germplasm cluster analysis whether based on 29 morphological traits or bulb yield-related traits could distinguish all germplasm. All accessions were divided into two groups with bolting and non-bolting respectively, or into five subgroups with different traits based on 29 morphological traits. Principal coordinate analysis based on eight bulb related traits divided all accessions into 6 groups. Yield among the accessions ranged from 1.60 to 16.78 t/ha, and three accessions yielded above 15 t/ha. Pearson analysis suggested bulb yield was significantly positively correlated with bulb weight (r = 0.99), bulb diameter (r = 0.73), bulb height (r = 0.53), clove number (r = 0.52), leaf width (r = 0.52). Allicin content ranged from 0.81 to 3.01 %. Pseudostem diameter was found to be significantly positively correlated with allicin content but with the low correlation coefficient (r = 0.23). The result will obviously be helpful for breeder and researchers to comprehensively understand the genetic background of the collection and more easily select the target accessions, especially those with high yield and allicin content.

Genetic characterization of an Italian Giant Reed ( Arundo donax L.) clones collection: exploiting clonal selection

Abstract: Arundo donax is a perennial rhizomatous plant growing spontaneously all over the world as an invasive plant reaching more than 8 m in height. It is a sterile plant which reproduces itself only agamically, through rhizomes and cane fragments which are transported by water or through human action. Although A. donax is an invasive plant it is considered one of the most promising energy crops, as it is characterized by a high energy balance. In this work we collected 87 A. donax clones from around Italy and with the aim of characterizing the genetic structure of the population, we studied the genetic diversity by using molecular markers (a survey of SSRs and genes from maize) and, for the first time, by sequence comparison using the purple plantl1 maize homologous orthologous gene. The results obtained showed a low genetic diversity as expected for an agamic plant. However, although MANTEL analysis did not show any statistical difference regarding the geographical distribution of these clones, we noticed by PCA/AMOVA analysis the presence of three different genotypes. Among a survey of eight clones studied in detail we found a high correlation between parent–progeny for the traits culm height and culm diameter and a heritability (h2) of the same traits respectively of 0.21 and 0.34 which appeared promising for clonal selection. Finally based on data collected regarding molecular analysis, chromosome number, epidermal cell size and chlorophyll content, we advance the hypothesis that A. donax may be a polyploid derived from Arundo plinii.

Sex chromosomes and quantitative sex expression in monoecious hemp (Cannabis sativa L.)

Abstract: Hemp (Cannabis sativa) has a highly variable sexual phenotype. In dioecious hemp, the sex is controlled by heteromorphic sex chromosomes according to an X-to-autosomes equilibrium. However, in monoecious hemp, the sex determinism remains widely unknown and has never been related to a quantitative approach of sex expression. The present paper aims to contribute to the comprehension of the sex determinism in monoecious hemp by assessing the genotypic variability of its sex expression and establishing its sex chromosomes. Five monoecious and one dioecious cultivars were grown in controlled conditions under several photoperiods. The monoecy degree of 194 monoecious plants was recorded at each node by a figure ranging from 0 (male flowers only) to 6 (female flowers only). The genome size of 55 plants was determined by flow cytometry. The DNA of 115 monoecious plants was screened with the male-associated marker MADC2. The monoecy degree varied significantly among monoecious cultivars from 3.36 ± 2.28 in 'Uso 31' to 5.70 ± 0.81 in the most feminised 'Epsilon 68'. The variation of monoecy degree among cultivars remained consistent across trials despite a significant "cultivar × trial" interaction and partly agreed with their earliness. The genome size of monoecious plants (1.791 ± 0.017 pg) was not different from that of females (1.789 ± 0.019 pg) but significantly lower than that of males (1.835 ± 0.019 pg). MADC2 was absent from all monoecious plants. These results strongly support that cultivars of monoecious hemp have the XX constitution and that their sex expression has a genetic basis. © 2013 Springer Science+Business Media Dordrecht.

New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi, a Saudi landrace into three African cultivars at the reproductive stage

Abstract: Salinity is a major constraint affecting rice productivity in rainfed and irrigated agro-ecosystems. Understanding salinity effects on rice production at the reproductive stage could improve adaptation for this trait. Identifying quantitative trait loci (QTLs) controlling adaptation to salinity may also accelerate breeding rice germplasm for environments prone to this stress. We used the salt tolerant landrace ‘Hasawi’ as a donor parent to generate three F2 offspring (consisting each of 500 individuals) with three African cultivars (‘NERICA-L-19’, ‘Sahel 108’ and ‘BG90-2’) used as recipient parents (RP). The F2s and F2:3s were evaluated for grain yield and other traits in saline fields. Salinity caused reduction in all measured traits across the F2-derived offspring, e.g. grain yield reduced between 65 and 73 %, but some offspring had twice the RP’s grain yield. QTL analysis revealed 75 QTLs for different traits in all 3 genetic backgrounds (GBs): 24 of them were common among all the 3 GBs while 31 were noted in 2 GBs, and 17 in one GB. ‘Hasawi’ contributed on average 49 % alleles to these QTLs. Two yield and yield related QTLs (qGY11 and qTN11) common in all 3 GBs were mapped on the same chromosomal segment suggesting these QTLs might be stable across different GBs. Four other QTLs were strongly associated with salinity tolerance with peak marker RM419, representing a potential candidate for MAS due to high LOD score and relatively large effect QTLs.

Comparative genotype reactions to Sclerotinia sclerotiorum within breeding populations of Brassica napus and B. juncea from India and China

Abstract: Twenty Brassica breeding populations derived from mass selection or inter-specific hybridization were field screened for resistance to three separate isolates of Sclerotinia sclerotiorum, the cause of Sclerotinia stem rot (SSR). Variation due to S. sclerotiorum isolates (P ≤ 0.001) and host populations (P ≤ 0.001) were highly significant. Populations × isolate interactions were also significant. S. sclerotiorum isolates, MBRS1 and MBRS5 were the most pathogenic and almost similar in terms of population reactions, with WW3 clearly being distinct and having a much smaller range in lesion length across the populations. There were wide ranging and variable responses in terms of resistance against S. sclerotiorum in Brassica napus and B. juncea, with or without B. carinata introgression, among these breeding populations. In B napus, ZY006 (resistant check) and Line6 (HZAU) were the most resistant, closely followed by Line1 (HZAU), OCRI-3 and Line5 (HZAU). Line6 (HZAU) showed excellent resistance against the highly virulent isolates MBRS1 and MBRS5; while OCRI-1 appeared most resistant against isolate WW3. The B. juncea × B. carinata hybrid JC134 (PAU) was the most resistant against isolate MBRS5 and B. juncea RH9902 × JN026 the most resistant against isolate MBRS1. B. napus lines Line2 (HZAU), Line4 (HZAU), OCRI-3; and OCRI-4, and the B. napus × B. carinata hybrid Surpass4000 NCB4 (PAU), showed a significant degree of isolate-dependency in their reactions. In contrast, some other genotypes such as B. napus lines Line1 (HZAU), OCRI-5; Ding 110× Oscar and, particularly, Line5 (HZAU), were largely isolate-independent, making them ideal sources of resistance to target and exploit in developing new commercial cultivars with more effective resistance to SSR across multiple pathotypes of this pathogen. Cluster analysis allowed categorization of the test populations into five groups, based on their resistant responses. B. napus ZY006 was the sole genotype in the most resistant group. B. napus lines Line6 (HZAU), Ding 110 × Oscar (HAU) and Line4 (HZAU) clustered in another genetically distinct resistant group. That lines could be grouped into those with similar responses across the three different isolates of S. sclerotiorum will save breeders much time and expense by eliminating duplication of breeding efforts that occurs from using genotypes that are essentially similar in terms of host resistance against this serious pathogen. Further, that populations of similar levels of resistance but narrow variation in the resistance range could be identified is significant, as these are most likely to reliably provide breeders with advanced populations that not only consistently display the level of resistance expected but also reflect genetic diversity of resistance sources needed to successfully develop new more-resistant commercial varieties.

Genetic control of yield and yield components in winter oilseed rape ( Brassica napus L.) grown under nitrogen limitation

Abstract: Despite its high nitrogen absorption capacity, oilseed rape (OSR) has a low apparent nitrogen use efficiency (NUE), which makes its production highly dependent on nitrogen fertilization. Improving NUE in OSR is therefore a main target in breeding. The objectives of the present work were to determine the genomic regions (QTLs) associated with yield and to assess their stability under contrasted nitrogen nutrition regimes. One mapping population, AM, was tested in a French location for three growing seasons (2011, 2012 and 2013), under two nitrogen conditions (optimal and low). Eight yield-related traits were scored and nitrogen-responsive traits were calculated. A total of 104 QTLs were detected of which 28 controlled flowering time and 76 were related to yield and yield components. Very few genotype × nitrogen interactions were detected and the QTLs were highly stable between the nitrogen conditions. In contrast, only a few QTLs were stable across the years of the trial, suggesting a strong QTL × year interaction. Finally, eleven critical genomic regions that were stable across nitrogen conditions and/or trial years were identified. One particular region located on the A5 linkage group appears to be a promising candidate for marker assisted selection programs. The different strategies for OSR breeding using the QTLs found in the present study are discussed.

Mapping of maternal QTLs for in vivo haploid induction rate in maize ( Zea mays L.)

Abstract: Haploid technology can significantly shorten the time required for inbred line improvement, accelerate the breeding process, and reduce breeding costs. The production of haploids is not only dependent on the genetics of the paternal haploid inducer, but it is also affected by the genetic background of the maternal donor during the process of haploid production. To address the maternal genetic contribution to haploid production, we pollinated a mapping population consisting of 186 F2:3 family lines derived from a cross between Zheng58 and Chang7-2 with the inducer line CAU5 and selected haploid kernels using R1-nj kernel markers. Two quantitative trait loci (QTLs), qmhir1 and qmhir2, which contribute to the maternal genetics of haploid induction, were detected on chromosomes 1 and 3, respectively. The qmhir1 locus is located between the flanking marker loci umc1292 and bnlg1014, and it explained 14.70 % of the phenotypic variation. The qmhir2 locus is located between marker loci umc1844 and umc2277 and it explained 8.42 % of the phenotypic variation. The genetic effect of both QTLs is partial dominance.

Comparative analysis of in vitro anther- and isolated microspore culture in hexaploid Triticale (X Triticosecale Wittmack) for androgenic parameters

Abstract: Two haploid induction media (190-0 and W14mi) were tested in isolated microspore culture of two triticale (X Triticosecale Wittmack) genotypes. The W14mi medium proved superior for the production of green plantlets in both genotypes. This basic medium (W14) was used to compare two doubled haploid production methods (isolated microspore culture and anther culture) with the same genotypes. The induction of androgenesis was more effective in isolated microspore culture than in anther culture. The number of embryo-like structures was 9.2 times higher in microspore culture (511.0/100 anthers) compared to anther culture (55.5/100 anthers) and the number of regenerant plantlets was also 3.4 times higher (anther culture—20.15/100 anthers; isolated microspore culture—67.6/100 anthers). However, the regenerant plantlets from isolated microspore culture were mainly albinos while predominantly green plantlets were regenerated from anther culture. The production of green plantlets from anther culture (16.8/100 anthers) was 2.9 times higher than from isolated microspore culture (5.8/100 anthers). The efficiency of anther culture was tested with eight winter triticale genotypes. The phenomenon of albinism did not hinder the green plant production in anther culture. Mean green plantlet production was 10.87/100 anthers. This value was two times higher than the number of albinos (5.01/100 anthers) and higher than previously published reports. The anther culture protocol described in this study is an efficient tool for the production of microspore-derived green plantlets in triticale.