Elite Breeding Research Articles

Enhancing the Nutritional Quality of Major Food Crops Through Conventional and Genomics-Assisted Breeding.

Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.

Performance of 16 Stevia rebaudiana seed cultigens for glycosides and yield in North Carolina

Currently, stevia (Stevia rebaudiana Bertoni) seeds are available to growers from many sources, but the origin of these populations is often unknown. Since stevia is a natural outcrosser, populations are heterozygous and heterogeneous. We were interested to characterize germplasm from 16 sources of stevia seeds for traits including yield, glycosides, and plant morphology, and then identify trait correlations. The cultigens evaluated were obtained from garden seed companies and commercial sources, and the trials were conducted for two years at two field locations. To quantify plant morphological traits, objective measurements were collected at two intervals to determine stem height, branching width, and leaf area. In addition, we screened for lodging and disease resistance, and yield before flowering stage. The cultigens tested were highly variable for yield and steviol glycosides, suggesting that a diverse genetic base is found among the population which is readily available to growers and breeders. High-yielding cultigens for biomass and glycoside concentration were identified. Cultigens with the highest yield and stability over years were seed-derived progeny from ‘Katupyry’, sourced from Stevia Store, and represent genetics useful in breeding for increased biomass. Cultigens with the highest glycoside level were NC-1003 and NC-1022, seed grown from Seed Savers, and could be used to improve desirable glycosides. This study highlights readily available seed cultigens that can be used to develop elite breeding populations.

Evaluation of durum wheat lines derived from interspecific crosses under drought and heat stress

AbstractThe productivity of durum wheat [Triticum turgidum subsp. durum (Desf.) van Slageren] is affected by drought and/or high temperatures, challenges to be amplified by climate change. Pre‐breeding using wild relatives can supply useful traits for durum wheat improvement to adapt to major abiotic and biotic stresses. Sixty‐seven lines issued from backcrosses of Cham5 and Haurani durum wheat varieties with accessions of Triticum aegilopoides (Link) Bal. ex Koern., T. dicoccoides Koern. ex Schweinf., T. urartu Thumanian ex Gandilyan, and Aegilops speltoides Tausch were evaluated for drought and heat tolerance. The trials were conducted during two seasons (2016−2017 and 2017–2018) at Tessaout, Morocco, under full irrigation (optimal conditions) and rainfed conditions (drought stressed) and at Wed Medani, Sudan, under full irrigation combined with heat stress. The recurrent parents, along with eight best cultivars and elite breeding lines, were used as checks. Drought reduced the grain yield by 62%. Grain yield and drought tolerance index were used to identify lines to be used by breeding programs to enhance drought and heat tolerance. The derivatives lines 142014 (Cham5*3/T. aegilopoides), 142074 (Cham5*3/T. dicoccoides), and 142015 along with the checks Icarachaz and Gidara 2 ranked among the best under heat stress. Under drought stress, the lines 141972 (Haurani*2/T. urartu) and 141973 (Cham5*2/T. dicoccoides) yielded 196 and 142% of their recurrent parents’ yield, respectively. High variation was found for agronomic and phenology traits, with heading time explaining 16% of grain yield under drought, while thousand kernel weight accounted for 18% of the yield under heat. We conclude that gene introgression from wild relatives pays off and can increase wheat resilience to cope with climate change effects.

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.).

Rye (Secale cereale L.) responds strongly to changes in heterozygosity with hybrids portraying strong heterosis effect on all developmental and yielding characteristics. In order to achieve the highest potential heterosis effect parental lines must originate from genetically distinct gene pools. Here we report the first comprehensive SNP-based population study of an elite germplasm using fertilization control system for hybrid breeding in rye that is genetically different to the predominating P-type. In total 376 inbred lines from Nordic Seed Germany GmbH were genotyped for 4419 polymorphic SNPs. The aim of this study was to confirm and quantify the genetic separation of parental populations, unveil their genetic characteristics and investigate underlying population structures. Through a palette of complimenting analysis, we confirmed a strong genetic differentiation (FST = 0.332) of parental populations validating the germplasms suitability for hybrid breeding. These were, furthermore, found to diverge considerably in several features with the maternal population portraying a strong population structure characterized by a narrow genetic profile, small effective population size and high genome-wise linkage disequilibrium. We propose that the employed male-sterility system putatively constitutes a population determining parameter by influencing the rate of introducing novel genetic variation to the parental populations. Functional analysis of linkage blocks led to identification of a conserved segment on the distal 4RL chromosomal region annotated to the Rfp3 male-fertility restoration 'Pampa' type gene. Findings of our study emphasized the immediate value of comprehensive population studies on elite breeding germplasms as a pre-requisite for application of genomic-based breeding techniques, introgression of novel material and to support breeder decision-making.

Detection of Quantitative Trait Loci (QTL) Associated with the Fruit Morphology of Tomato.

Tomato (Solanum lycopersicum L.) is the second most-consumed vegetable in the world. The market value and culinary purpose of tomato are often determined by fruit size and shape, which makes the genetic improvement of these traits a priority for tomato breeders. The main objective of the study was to detect quantitative trait loci (QTL) associated with the tomato fruit shape and size. The use of elite breeding materials in the genetic mapping studies will facilitate the detection of genetic loci of direct relevance to breeders. We performed QTL analysis in an intra-specific population of tomato developed from a cross between two elite breeding lines NC 30P × NC-22L-1(2008) consisting of 110 recombinant inbred lines (RIL). The precision software Tomato Analyzer (TA) was used to measure fruit morphology attributes associated with fruit shape and size traits. The RIL population was genotyped with the SolCAP 7720 SNP array. We identified novel QTL controlling elongated fruit shape on chromosome 10, explaining up to 24% of the phenotypic variance. This information will be useful in improving tomato fruit morphology traits.

The Dawn of the Age of Multi-Parent MAGIC Populations in Plant Breeding: Novel Powerful Next-Generation Resources for Genetic Analysis and Selection of Recombinant Elite Material.

The compelling need to increase global agricultural production requires new breeding approaches that facilitate exploiting the diversity available in the plant genetic resources. Multi-parent advanced generation inter-cross (MAGIC) populations are large sets of recombinant inbred lines (RILs) that are a genetic mosaic of multiple founder parents. MAGIC populations display emerging features over experimental bi-parental and germplasm populations in combining significant levels of genetic recombination, a lack of genetic structure, and high genetic and phenotypic diversity. The development of MAGIC populations can be performed using “funnel” or “diallel” cross-designs, which are of great relevance choosing appropriate parents and defining optimal population sizes. Significant advances in specific software development are facilitating the genetic analysis of the complex genetic constitutions of MAGIC populations. Despite the complexity and the resources required in their development, due to their potential and interest for breeding, the number of MAGIC populations available and under development is continuously growing, with 45 MAGIC populations in different crops being reported here. Though cereals are by far the crop group where more MAGIC populations have been developed, MAGIC populations have also started to become available in other crop groups. The results obtained so far demonstrate that MAGIC populations are a very powerful tool for the dissection of complex traits, as well as a resource for the selection of recombinant elite breeding material and cultivars. In addition, some new MAGIC approaches that can make significant contributions to breeding, such as the development of inter-specific MAGIC populations, the development of MAGIC-like populations in crops where pure lines are not available, and the establishment of strategies for the straightforward incorporation of MAGIC materials in breeding pipelines, have barely been explored. The evidence that is already available indicates that MAGIC populations will play a major role in the coming years in allowing for impressive gains in plant breeding for developing new generations of dramatically improved cultivars.

Seed quality of 22 quinoa materials (Chenopodium quinoa Willd.) from the department of Boyacá

ABSTRACT Chenopodium quinoa Willd. is a pseudocereal with seeds that are a rich source of vitamins and minerals. However, there are few studies on quinoa seed quality, especially for the Colombian germplasm. So, the objective of this research was to determine the quality of 22 quinoa materials from the Department of Boyaca by evaluating the physical (color, shape and diameter) and physiological (tetrazolium test) quality of the seeds. It was found that 36% of the materials had a white grain color, 80% cylindrical shape, 65% smooth edges and diameters smaller than 2mm, desirable characteristics for post-harvest processes. The evaluated physical characteristics presented high variability between the evaluated materials, which is desirable for elite breeding processes. The imbibition rate showed that germination was rapid (at 4 hours, the weight of the seeds doubled), that is, the materials were not dormant. Finally, it was determined that storage conditions, such as temperature and relative humidity, are essential for preventing deterioration in quinoa seeds; these factors can also affect germination and long-term vigor.

Adaptive Traits to Improve Durum Wheat Yield in Drought and Crown Rot Environments.

Durum wheat (Triticum turgidum L. ssp. durum) production can experience significant yield losses due to crown rot (CR) disease. Losses are usually exacerbated when disease infection coincides with terminal drought. Durum wheat is very susceptible to CR, and resistant germplasm is not currently available in elite breeding pools. We hypothesize that deploying physiological traits for drought adaptation, such as optimal root system architecture to reduce water stress, might minimize losses due to CR infection. This study evaluated a subset of lines from a nested association mapping population for stay-green traits, CR incidence and yield in field experiments as well as root traits under controlled conditions. Weekly measurements of normalized difference vegetative index (NDVI) in the field were used to model canopy senescence and to determine stay-green traits for each genotype. Genome-wide association studies using DArTseq molecular markers identified quantitative trait loci (QTLs) on chromosome 6B (qCR-6B) associated with CR tolerance and stay-green. We explored the value of qCR-6B and a major QTL for root angle QTL qSRA-6A using yield datasets from six rainfed environments, including two environments with high CR disease pressure. In the absence of CR, the favorable allele for qSRA-6A provided an average yield advantage of 0.57 t·ha−1, whereas in the presence of CR, the combination of favorable alleles for both qSRA-6A and qCR-6B resulted in a yield advantage of 0.90 t·ha−1. Results of this study highlight the value of combining above- and belowground physiological traits to enhance yield potential. We anticipate that these insights will assist breeders to design improved durum varieties that mitigate production losses due to water deficit and CR.

Assessment of Genetic Diversity and Population Structure of Rice Donor Germplasm Accessions in the Philippines

Genetic diversity is necessary to safeguard potentially vital traits for adaptation to environmental stresses and a proximate defense against a resurgence of pests and diseases amid climate change. The hybridization core germplasm of the Philippine Rice Research Institute (PhilRice) comprises local and foreign landraces, varieties, and elite breeding lines, which are various sources for diversification and creation of superior rice varieties. The objective of the study is to investigate the level of genetic diversity and population structure across 472 parental germplasm using 17 polymorphic simple sequence repeat (SSR) markers as assistance for rice breeders in the selection of unique parents for hybridization. Germplasm accessions showed high genetic diversity (71%) and formed a structure delineating indica, temperate japonica, and tropical japonica – with 32.8% admixtures identified through the distance-based neighbor-joining (NJ) method, model-based Bayesian structure, and discriminant analysis of principal components (DAPC). Analysis of molecular variance (AMOVA) revealed that the majority of the variation (87.0%) was attributed to accession differences within a population, indicating regular seed movement limited to each subgroup rather than between population (8.7%), wherein the highest fixation index (FST) was observed between tropical and temperate japonica (FST = 0.13). The study established a PhilRice parental germplasm collection containing 306 genetically pure accessions retaining the majority of genetic diversity from the first collection, which offers a promising aid in generating favorable genetic gain through careful genotypic selection in rice breeding programs.

Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress.

In plant and animal breeding, genomic prediction models are established to select new lines based on genomic data, without the need for laborious phenotyping. Prediction models can be trained on recent or historic phenotypic data and increasingly available genotypic data. This enables the adoption of genomic selection also in under-used legume crops such as common bean. Beans are an important staple food in the tropics and mainly grown by smallholders under limiting environmental conditions such as drought or low soil fertility. Therefore, genotype-by-environment interactions (G × E) are an important consideration when developing new bean varieties. However, G × E are often not considered in genomic prediction models nor are these models implemented in current bean breeding programs. Here we show the prediction abilities of four agronomic traits in common bean under various environmental stresses based on twelve field trials. The dataset includes 481 elite breeding lines characterized by 5,820 SNP markers. Prediction abilities over all twelve trials ranged between 0.6 and 0.8 for yield and days to maturity, respectively, predicting new lines into new seasons. In all four evaluated traits, the prediction abilities reached about 50–80% of the maximum accuracies given by phenotypic correlations and heritability. Predictions under drought and low phosphorus stress were up to 10 and 20% improved when G × E were included in the model, respectively. Our results demonstrate the potential of genomic selection to increase the genetic gain in common bean breeding. Prediction abilities improved when more phenotypic data was available and G × E could be accounted for. Furthermore, the developed models allowed us to predict genotypic performance under different environmental stresses. This will be a key factor in the development of common bean varieties adapted to future challenging conditions.

English

Forty-nine tef, Eragrostis tef (Zucc.) Trotter, genotypes comprising 36 improved and 10 farmers’ varieties, and, three elite breeding lines were field evaluated using 7 × 7 simple lattice design at two contrasting locations (Debre Zeit and Alem Tena) in central Ethiopia during the main cropping season. The objective was to assess the extent and pattern of genetic diversity for 23 quantitative pheno-agro-morphological traits. Differences among the varieties were significant for most of the traits except lodging index, thousand seed weight, plant weight and grain yield per plant at each location. Similarity, the pooled analysis over locations showed significant genotype effect for most of the traits except number of total and fertile tillers, lodging index, plant weight and grain yield per plant. The varieties were grouped into seven clusters of different sizes. Improved varieties resulting from direct selection and hybridization were clustered together while local varieties mostly remained solitary. Principal component analysis depicted cumulative effects of a number of traits resulted in the differentiation of the varieties into clusters. Genetic distances among most of the clusters were significant such that crosses between parents selected out of them are expected to generate desirable genetic recombination. Hence, incorporation of farmers’ varieties in the breeding program would be imperative for broadening the genetic base of the released varieties. Moreover, future research strategies on germplasm collection, conservation, rejuvenation, characterization, selection and incorporation must be given due emphasis in the tef breeding program. Key words: Clustering, genetic diversity, improved varieties, farmers’ varieties, pheno-agro-morphological traits, principal component analysis, tef. &nbsp

Highlights of strategies adapted by two Pennisetum glaucum (L.) R. Br. races in a simulated drought stress experiment

Pearl millet (Pennisetum glaucum) is an important staple food crop in Asia and Africa. The most severe abiotic stress that hinders growth and development of crop is Drought. Four genotypes of P. glaucum were grown for 4 weeks in a greenhouse facility with the aim to identify several physiological responses observed after 12 days of drought stress and transcriptional profiling related to drought tolerance. Distinct parameters like relative water content (RWC), water use efficiency (WUE), stomata quantification (SI%), electron transport rate (ETR), photochemical (qP) and non-photochemical quenching (qNP) were measured under simulated drought condition for the selected four genotypes. The genotypes were grouped into two pearl millet races viz., nigritarum and globosum. Genotype 1P35451 of the nigritarum race showed augmentation in dry weight (DW) and tolerance index (TI) under the condition of decreased soil water due to transpiration. It exhibited a remarkable ability for recovery of leaf after an imposed drought condition in RWC, WUE and SI. Also, the transcriptional expression of CBF, RubSc and PIP 2;3 genes indicated that they were quick to respond to drought. CBF gene has proven to be useful for evaluating the ability to withstand drought in both races. RubSc and PIP2:3 displayed a pronounced increase in their expression level in nigritarum race. However, the drought tolerant genotype 1P13013 of globosum functioned in stomatal movement which is well linked with the expression of the Nicotinamide Adenine Dinucleotide Phosphate (NADP) enzyme. Therefore, the results indicate that mRNA expression of genes in both races under drought stress provides information on their ability to resist drought and could supply valuable molecular information for drought-tolerant elite breeding programs in the future.

Genetic Resources, Breeding Programs in China, and Gene Mining of Peach: A Review

ABSTRACT Research on peach genetic resources and breeding has achieved remarkable progress in recent decades, especially in China. In this review, we first described the geographic distribution, ecology, phenotypes, and genetic diversity of peach landraces and wild relatives in China. We also discussed the almond. Subsequently, breeding programs of peaches in China are summarized, including breeding history, breeding targets, breeding institutes, elite breeding materials, breeding solutions, and domestically bred representative cultivars. Furthermore, we reviewed the genes or loci that have been mined using both linkage mapping and genome wide association study (GWAS) as well as the evolutionary genetics and domestication history of the peach. Finally, we gave our perspectives and suggestions for future breeding in terms of breeding material selection and breeding technology innovation.

Optimized breeding strategies to harness genetic resources with different performance levels

BackgroundThe narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient strategy is required to broaden the genetic base of commercial breeding programs while not compromising short-term variety release. Optimal cross selection aims at identifying the optimal set of crosses that balances the expected genetic value and diversity. We propose to consider genomic selection and optimal cross selection to recurrently improve genetic resources (i.e. pre-breeding), to bridge the improved genetic resources with elites (i.e. bridging), and to manage introductions into the elite breeding population. Optimal cross selection is particularly adapted to jointly identify bridging, introduction and elite crosses to ensure an overall consistency of the genetic base broadening strategy.ResultsWe compared simulated breeding programs introducing donors with different performance levels, directly or indirectly after bridging. We also evaluated the effect of the training set composition on the success of introductions. We observed that with recurrent introductions of improved donors, it is possible to maintain the genetic diversity and increase mid- and long-term performances with only limited penalty at short-term. Considering a bridging step yielded significantly higher mid- and long-term genetic gain when introducing low performing donors. The results also suggested to consider marker effects estimated with a broad training population including donor by elite and elite by elite progeny to identify bridging, introduction and elite crosses.ConclusionResults of this study provide guidelines on how to harness polygenic variation present in genetic resources to broaden elite germplasm.

Genetic mapping of the common and dwarf bunt resistance gene Bt12 descending from the wheat landrace PI119333

Common bunt (CB), caused by Tilletia caries and T. foetida, and dwarf bunt (DB), caused by T. controversa, are particularly destructive diseases of wheat grown under organic (low-input) production conditions and negatively affect both grain yield and quality. A total of 16 race specific bunt resistance genes have been proposed to date. Thereof, only Bt9 and Bt10 have been mapped so far. A mapping and two validation populations comprising 176 recombinant inbred lines were evaluated for CB and DB in artificially inoculated field trials. The mapping population was derived from the cross of the Bt12 carrier PI119333 and the susceptible cultivar ‘Rainer’. The population was genotyped with the Illumina 15 K SNP chip and the major QTL QBt.ifa-7DS representing Bt12 was identified on chromosome 7DS, explaining 39% and 14% of the phenotypic variation for CB and DB resistance, respectively. Selected SNP markers were turned into Kompetitive Allele-Specific (KASP) markers and used to validate Bt12 in two independent validation populations. These markers can be used for introgressing Bt12 into regionally adapted elite breeding material.

Host Induced Gene Silencing Targeting Aspergillus flavus aflM Reduced Aflatoxin Contamination in Transgenic Maize Under Field Conditions.

Maize (Zea mays L.) is one of the major crops susceptible to Aspergillus flavus infection and subsequent contamination with aflatoxins, the most potent naturally produced carcinogenic secondary metabolites. This pathogen can pose serious health concerns and cause severe economic losses due to the Food and Drug Administration (FDA) regulations on permissible levels of aflatoxins in food and feed. Although biocontrol has yielded some successes in managing aflatoxin contamination, enhancing crop resistance is still the preferred choice of management for long-term sustainability. Hence, host induced gene silencing (HIGS) strategy was explored in this study. The A. flavus gene aflM encoding versicolorin dehydrogenase, a key enzyme involved in the aflatoxin biosynthetic pathway, was selected as a possible target for suppression through HIGS. An RNAi vector containing a portion of the aflM gene was constructed and introduced into immature B104 maize zygotic embryos through Agrobacterium transformation. PCR analysis of the genomic DNA from T0 leaf tissue confirmed the presence of the transgene in six out of the seven events. The seeds from the lines that showed reduced aflatoxin production in laboratory aflatoxin kernel screening assay (KSA) have been increased from T1 to T4 generation in the past four years. Changes in aflatoxin resistance in these transgenic kernels have been evaluated under both field and laboratory conditions. The T2 generation kernels containing the transgene from two events out of four examined had less aflatoxin (P ≤ 0.01 and P ≤ 0.08) than those without the transgene. Field-inoculated homozygous T3 and T4 transgenic kernels also revealed lower levels of aflatoxins (P ≤ 0.04) than kernels from the null (segregated non-transgenic samples) or B104 controls. A similar result was observed when the harvested T3 and T4 homozygous transgenic kernels were evaluated under KSA conditions without inoculation (P ≤ 0.003–0.05). These two events were crossed with LH195, LH197, LH210, and PHW79 elite breeding lines and the resulting crosses supported less aflatoxin (P ≤ 0.02) than the crosses made with non-transgenic lines. In addition, significantly higher levels of aflM gene-specific small RNAs were detected in the transgenic leaf and kernel tissues, indicating that the enhanced aflatoxin resistance in the homozygous transgenic kernels is likely due to suppression of aflM expression through HIGS.

Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed Down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.).

The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.

Molecular Genetics, Genomics, and Biotechnology in Crop Plant Breeding

A diverse set of molecular markers techniques have been developed over the last almost 40 years and used with success for breeding a number of major crops. These have been narrowed down to a few preferred DNA based marker types, and emphasis is now on adapting the technologies to a wide range of crop plants and trees. In this Special Issue, the strength of molecular breeding is revealed through research and review papers that use a combination of molecular markers with other classic breeding techniques to obtain quality improvement of the crop. The constant improvement and maintenance of quality by breeding is crucial and challenged by a changing climate and molecular markers can support the direct introgression of traits into elite breeding lines. All the papers in this Special Issue “Molecular genetics, Genomics, and Biotechnology in Crop Plant Breeding” have attracted significant attention, as can be witnessed by the graphs for each paper on the Journal’s homepage. It is the hope that it will encourage others to use these tools in developing an even wider range of crop plants and trees.

Character association and genetic divergence study in elite breeding lines of groundnut (Arachis hypogaea L.)

Character association and genetic divergence were carried out in a set of elite breeding lines of groundnut. Podyield/plant showed significant positive correlation with days to first flowering, plant height, total number ofgynophores/plant and 100 kernel weight both at phenotypic and genotypic level. Biological yield and harvest index had higher positive correlation as well as direct positive effect with seed yield. Thirty genotypes were distributed into eight clusters out of which four were mono-genotypic. Cluster I consisted of 16 genotypes, whereas cluster II, III and IV consisted four, four and two genotypes respectively. Cluster VIII showed highest pod yield/plant followed by cluster IV. Inter cluster distance between cluster VI and VIII was highest, whereas lowest inter cluster distance was observed between cluster III and I. Pod yield /plant contributed maximum towards genetic divergence followed by yield (q/ha).

Dissection of Superior Alleles for Yield-Related Traits and Their Distribution in Important Cultivars of Wheat by Association Mapping.

Uncovering the genetic basis of yield-related traits is important for molecular improvement of wheat cultivars. In this study, a genome-wide association study was conducted using the wheat 55K genotyping assay and a diverse panel of 384 wheat genotypes. The accessions used included 18 founder parents and 15 widely grown cultivars with annual maximum acreages of over 667,000 ha, and the remaining materials were elite cultivars and breeding lines from several major wheat ecological areas of China. Field trials were conducted in five major wheat ecological regions of China over three consecutive years. A total of 460 significant loci were detected for eight yield-related traits. Forty-five superior alleles distributed over 31 loci for which differences in phenotypic values grouped by single nucleotide polymorphism (SNP) reached significant levels (P < 0.05) in nine or more environments, were detected; some of these loci were previously reported. Eleven of the 31 superior allele loci on chromosomes 4A, 5A, 3B, 5B, 6B, 7B, 5D, and 7D had pleiotropic effects. For example, AX-95152512 on 5D was simultaneously related to increased grain weight per spike (GWS) and decreased plant height (PH); AX-109860828 on 5B simultaneously led to a high 1,000-kernel weight (TKW) and short PH; and AX-111600193 on 4A was simultaneously linked to a high TKW and GWS, and short PH. The favorable alleles in each accession ranged from 2 to 30 with an average of 16 at the thirty-one loci in the population, and six accessions (Zhengzhou683, Suzhou7829, Longchun7, Ningmai6, Yunmai35 and Zhen7630) contained more than 27 favorable alleles. A significant association between the number of favorable alleles and yield was observed (r = 0.799, p < 0.0001), suggesting that pyramiding multiple QTL with marker-assisted selection may effectively increase yield of wheat. Furthermore, distribution of superior alleles in founder parents and widely grown cultivars was also discussed here. This study is useful for marker-assisted selection for yield improvement and dissecting the genetic mechanism of important cultivars in wheat.