Architecture Of Grain Yield Research Articles

Molecular mechanisms of drought resistance using genome-wide association mapping in maize (Zea mays L.)

BackgroundDrought is a critical abiotic stress that influences maize yield and reduces grain yield when it occurs at the flowering or filling stage. To dissect the genetic architecture of grain yield under drought stress (DS), a genome-wide association analysis was conducted in a maize population composed of diverse inbred lines from five locations under well-watered and DS conditions at flowering in 2019 and 2020.ResultsUsing a fixed and random model circulating probability unification model, a total of 147 loci associated with grain yield or the drought resistance index (DRI) were identified, of which 54 loci were associated with a DRI with an average phenotypic variation explanation of 4.03%. Further, 10 of these loci explained more than 10% of the phenotypic variation. By integrating two public transcriptome datasets, 22 differentially expressed genes were considered as candidate genes, including the cloned gene ZmNAC49, which responds to drought by regulating stomatal density. Enrichment and protein interaction network showed that signaling pathways responded to drought resistance, including jasmonic acid and salicylic acid, mitogen-activated protein kinase, and abscisic acid-activated. Additionally, several transcription factors involved in DS were identified, including basic leucine zipper (GRMZM2G370026), NAC (GRMZM2G347043), and ethylene-responsive element binding protein (GRMZM2G169654).ConclusionsIn this study, we nominated several genes as candidate genes for drought resistance by intergrating association maping and transcription analysis. These results provide valuable information for understanding the genetic basis of drought tolerance at the mature stage and for designing drought-tolerant maize breeding.

Genetic Architecture of Grain Yield and Some of Its Components Traits in Maize (Zea mays L.)

Six inbred lines of maize (ZP-595, DKC-6418, DK-17, ZP-694, Sgporo from panan and UN 4652) were included in a half diallel cross. The inbred lines and their 15 crosses were planted in the fields of the College of Agricultural Engineering Sciences, Duhok University on July 5, 2018, using randomized complete block design with three replications. The components of phenotypic variance and narrow sense heritability were estimated, and the regression line analysis method was adopted for the traits: number of days to silking, number of days to tasseling, plant height, upper ear height, leaf area, number of rows. ear-1, number of grains. row-1, grain yield. Plant-1, weight of 300 grains, and shelling percent. The results showed that the mean square of the genotypes (parents and hybrids) was highly significant for all traits. The regression coefficient of Wr on Vr appeared significant for all traits except leaf area, indicating the presence of epistasis in its inheritance. It is also evident that the variances, additive (D) and dominant components (H1 and H2) were significant from zero for all traits, indicating the importance of additive and non-additive gene action in the inheritance of these traits. It was shown from Wr, Vr regression line analysis that the regression line cutting the Wr axis above the origin point for number of days to silking, number of days to tasseling, plant height, upper ear height, leaf area, number of rows. ear-1 and shelling percent, an indication of the additive effect of genes with a decrease in dominance, while the regression line crossed the Wr axis under the origin point, for number of grains. Ear-1, grain yield. Plant-1 and shelling percent indicating the presence of over dominance with proportions of dominant and recessive genes in parents. The narrow sense heritability was low for number of rows. ear-1, number of grains. Ear-1, grain yield. Plant-1, 300 grains weight and shelling percent, moderate for upper ear height and leaf area and high for number of days to silking, number of days to tasseling and plant height.
 

Genetic Architecture of Grain Yield and Some of Its Components Traits in Maize (Zea mays L.)

Six inbred lines of maize (ZP-595, DKC-6418, DK-17, ZP-694, Sgporo from panan and UN 4652) were included in a half diallel cross. The inbred lines and their 15 crosses were planted in the fields of the College of Agricultural Engineering Sciences, Duhok University on July 5, 2018, using randomized complete block design with three replications. The components of phenotypic variance and narrow sense heritability were estimated, and the regression line analysis method was adopted for the traits: number of days to silking, number of days to tasseling, plant height, upper ear height, leaf area, number of rows. ear-1, number of grains. row-1, grain yield. Plant-1, weight of 300 grains, and shelling percent. The results showed that the mean square of the genotypes (parents and hybrids) was highly significant for all traits. The regression coefficient of Wr on Vr appeared significant for all traits except leaf area, indicating the presence of epistasis in its inheritance. It is also evident that the variances, additive (D) and dominant components (H1 and H2) were significant from zero for all traits, indicating the importance of additive and non-additive gene action in the inheritance of these traits. It was shown from Wr, Vr regression line analysis that the regression line cutting the Wr axis above the origin point for number of days to silking, number of days to tasseling, plant height, upper ear height, leaf area, number of rows. ear-1 and shelling percent, an indication of the additive effect of genes with a decrease in dominance, while the regression line crossed the Wr axis under the origin point, for number of grains. Ear-1, grain yield. Plant-1 and shelling percent indicating the presence of over dominance with proportions of dominant and recessive genes in parents. The narrow sense heritability was low for number of rows. ear-1, number of grains. Ear-1, grain yield. Plant-1, 300 grains weight and shelling percent, moderate for upper ear height and leaf area and high for number of days to silking, number of days to tasseling and plant height.

Study of genetic architecture of grain yield and quality traits through generation mean analysis in rice (Oryza sativa L.)

A perusal of gene effects in generation mean analysis for three crosses viz., BPT 5204 x IR 36, BPT 5204 x NLR 34449 and RNR 2465 x IR 64 revealed the presence of a significant proportion of epistatic effects besides the major components viz., additive (d) and dominance (h) gene effects for important yield and quality attributes. Partitioning of variance indicating that the mean values (m) for gene effects were highly significant in all the three crosses for most of the traits, the results of dominance (h) and dominance × dominance (l) type interactions revealed that duplicate type of epistasis was prevalent for most of the traits in all the six crosses except in RNR 2465 x IR 64 for the number of filled grains per panicle; BPT 5204 x NLR 34449 for kernel breadth and kernel elongation ratio and BPT 5204 x IR 36 for harvest index where, complementary gene action played a vital role in the inheritance of the traits. Therefore, improvement of these traits appears to overwhelmed with difficulties as simple selection techniques will not be able to fix superior lines in the early segregating generations. Postponement of selection for superior lines to later generations in pedigree breeding will be effective. However, one or two cycles of recurrent selection followed by pedigree breeding will be effective and useful to utilize both additive and non-additive gene effects. The predominance of dominance and epistatic interactions in all the crosses for quality traits indicates that selection would be more effective if the dominance and epistatic effects are first reduced by a few generations of selfing.  Keywords: Rice, generation mean analysis, gene action

High-resolution detection of quantitative trait loci for seven important yield-related traits in wheat (Triticum aestivum L.) using a high-density SLAF-seq genetic map

BackgroundYield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with grain yield of wheat (Triticum aestivum L.). To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six/eight environments.ResultsA total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multi-environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked with five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search.ConclusionsSix major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grain yield and developing new wheat varieties with high and stable yield in wheat.

The Genetic Architecture of Grain Yield in Spring Wheat Based on Genome-Wide Association Study.

Uncovering the genetic architecture for grain yield (GY)–related traits is important for wheat breeding. To detect stable loci for GY-related traits, a genome-wide association study (GWAS) was conducted in a diverse panel, which included 251 elite spring wheat accessions mainly from the Northeast of China. In total, 52,503 single nucleotide polymorphisms (SNPs) from the wheat 55 K SNP arrays were used. Thirty-eight loci for GY-related traits were detected and each explained 6.5–16.7% of the phenotypic variations among which 12 are at similar locations with the known genes or quantitative trait loci and 26 are likely to be new. Furthermore, six genes possibly involved in cell division, signal transduction, and plant development are candidate genes for GY-related traits. This study provides new insights into the genetic architecture of GY and the significantly associated SNPs and accessions with a larger number of favorable alleles could be used to further enhance GY in breeding.

Genetic architecture of maize yield traits dissected by QTL mapping and GWAS in maize

The study of yield traits can reveal the genetic architecture of grain yield for improving maize production. In this study, an association panel comprising 362 inbred lines and a recombinant inbred line population derived from X178 × 9782 were used to identify candidate genes for nine yield traits. High-priority overlap (HPO) genes, which are genes prioritized in a genome-wide association study (GWAS), were investigated using coexpression networks. The GWAS identified 51 environmentally stable SNPs in two environments and 36 pleiotropic SNPs, including three SNPs with both attributes. Seven hotspots containing 41 trait-associated SNPs were identified on six chromosomes by permutation. Pyramiding of superior alleles showed a highly positive effect on all traits, and the phenotypic values of ear diameter and ear weight consistently corresponded with the number of superior alleles in tropical and temperate germplasm. A total of 61 HPO genes were detected after trait-associated SNPs were combined with the coexpression networks. Linkage mapping identified 16 environmentally stable and 16 pleiotropic QTL. Seven SNPs that were located in QTL intervals were assigned as consensus SNPs for the yield traits. Among the candidate genes predicted by our study, some genes were confirmed to function in seed development. The gene Zm00001d016656 encoding a serine/threonine protein kinase was associated with five different traits across multiple environments. Some genes were uniquely expressed in specific tissues and at certain stages of seed development. These findings will provide genetic information and resources for molecular breeding of maize grain yield.

Genetic architecture of phenotypic indices for simultaneous improvement of protein content and grain yield in triticale (×triticosecale)

AbstractOur study aimed to assess the potential of indices, including grain protein deviation and protein yield, to simultaneously improve grain yield and protein content in triticale. Our analysis of 1.218 triticale genotypes revealed significant genotypic variation and high heritabilities for all traits. We analysed the suitability of the indices for phenotypic selection for both high grain yield and increased protein content. We show that some genotypes were selected irrespective of the applied index, but also observed considerable differences between the indices. To uncover the genetic architecture of grain yield, protein content and derived indices, we performed genome‐wide association mapping and biparental QTL mapping. This revealed many pleiotropic QTL with opposite effects on grain yield and protein content and a complex inheritance of all traits, suggesting that the genetic architecture limits the potential of marker‐assisted selection. Nevertheless, the use of these indices is recommended for breeding of special‐purpose cultivars, like high‐protein cultivars for on‐farm feed production.

Haplotype-Based, Genome-Wide Association Study Reveals Stable Genomic Regions for Grain Yield in CIMMYT Spring Bread Wheat.

We untangled key regions of the genetic architecture of grain yield (GY) in CIMMYT spring bread wheat by conducting a haplotype-based, genome-wide association study (GWAS), together with an investigation of epistatic interactions using seven large sets of elite yield trials (EYTs) consisting of a total of 6,461 advanced breeding lines. These lines were phenotyped under irrigated and stress environments in seven growing seasons (2011–2018) and genotyped with genotyping-by-sequencing markers. Genome-wide 519 haplotype blocks were constructed, using a linkage disequilibrium-based approach covering 14,036 Mb in the wheat genome. Haplotype-based GWAS identified 7, 4, 10, and 15 stable (significant in three or more EYTs) associations in irrigated (I), mild drought (MD), severe drought (SD), and heat stress (HS) testing environments, respectively. Considering all EYTs and the four testing environments together, 30 stable associations were deciphered with seven hotspots identified on chromosomes 1A, 1B, 2B, 4A, 5B, 6B, and 7B, where multiple haplotype blocks were associated with GY. Epistatic interactions contributed significantly to the genetic architecture of GY, explaining variation of 3.5–21.1%, 3.7–14.7%, 3.5–20.6%, and 4.4– 23.1% in I, MD, SD, and HS environments, respectively. Our results revealed the intricate genetic architecture of GY, controlled by both main and epistatic effects. The importance of these results for practical applications in the CIMMYT breeding program is discussed.

Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population.

A multiparental random mating population used in sorghum breeding is amenable for the detection of QTLs related to tropical soil adaptation, fine mapping of underlying genes and genomic selection approaches. Tropical soils where low phosphorus (P) and aluminum (Al) toxicity limit sorghum [Sorghum bicolor (L.) Moench] production are widespread in the developing world. We report on BRP13R, a multiparental random mating population (MP-RMP), which is commonly used in sorghum recurrent selection targeting tropical soil adaptation. Recombination dissipated much of BRP13R's likely original population structure and average linkage disequilibrium (LD) persisted up to 2.5Mb, establishing BRP13R as a middle ground between biparental populations and sorghum association panels. Genome-wide association mapping (GWAS) identified conserved QTL from previous studies, such as for root morphology and grain yield under low-P, and indicated the importance of dominance in the genetic architecture of grain yield. By overlapping consensus QTL regions, we mapped two candidate P efficiency genes to a ~ 5Mb region on chromosomes 6 (ALMT) and 9 (PHO2). Remarkably, we find that only 200 progeny genotyped with ~ 45,000 markers in BRP13R can lead to GWAS-based positional cloning of naturally rare, subpopulation-specific alleles, such as for SbMATE-conditioned Al tolerance. Genomic selection was found to be useful in such MP-RMP, particularly if markers in LD with major genes are fitted as fixed effects into GBLUP models accommodating dominance. Shifts in allele frequencies in progeny contrasting for grain yield indicated that intermediate to minor-effect genes on P efficiency, such as SbPSTOL1 genes, can be employed in pre-breeding via allele mining in the base population. Therefore, MP-RMPs such as BRP13R emerge as multipurpose resources for efficient gene discovery and deployment for breeding sorghum cultivars adapted to tropical soils.

Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel

BackgroundReproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers.ResultsThe study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought.ConclusionThese results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

Long‐term trends and genetic architecture of seed characteristics, grain yield and correlated agronomic traits in triticale (×Triticosecale Wittmack)

AbstractThe aim of this study was to investigate long‐term genetic trends and the genetic architecture of grain yield, seed characteristics and correlated agronomic traits in triticale. Therefore, a panel of 846 diverse triticale genotypes was assessed for three agronomic and three seed shape‐ and size‐related traits. We observed a high genotypic variation and a high heritability for all traits. Analysing the development of these traits during the last decades revealed a continuous increase for grain yield and thousand‐kernel weight, and a slight increase in seed width. The seed characteristics and thousand‐kernel weight formed a complex of highly positive correlated traits. Genome‐wide association mapping revealed many small‐effect QTL and a few moderate‐effect QTL. The allele frequencies of the moderate‐effect QTL followed the same temporal trends as observed for the phenotype. In line with the phenotypic correlations, we identified several pleiotropic QTL for grain yield, thousand‐kernel weight, seed width and seed area. Our results illustrate the continuous progress achieved in triticale breeding and suggest that triticale seeds have been selected to be more spherical in modern cultivars.

Incorporating Genome-Wide Association Mapping Results Into Genomic Prediction Models for Grain Yield and Yield Stability in CIMMYT Spring Bread Wheat.

Untangling the genetic architecture of grain yield (GY) and yield stability is an important determining factor to optimize genomics-assisted selection strategies in wheat. We conducted in-depth investigation on the above using a large set of advanced bread wheat lines (4,302), which were genotyped with genotyping-by-sequencing markers and phenotyped under contrasting (irrigated and stress) environments. Haplotypes-based genome-wide-association study (GWAS) identified 58 associations with GY and 15 with superiority index Pi (measure of stability). Sixteen associations with GY were “environment-specific” with two on chromosomes 3B and 6B with the large effects and 8 associations were consistent across environments and trials. For Pi, 8 associations were from chromosomes 4B and 7B, indicating ‘hot spot’ regions for stability. Epistatic interactions contributed to an additional 5–9% variation on average. We further explored whether integrating consistent and robust associations identified in GWAS as fixed effects in prediction models improves prediction accuracy. For GY, the model accounting for the haplotype-based GWAS loci as fixed effects led to up to 9–10% increase in prediction accuracy, whereas for Pi this approach did not provide any advantage. This is the first report of integrating genetic architecture of GY and yield stability into prediction models in wheat.

Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population

Identification of Quantitative Trait Loci (QTL) has been a challenge for complex traits due to the use of populations with narrow genetic base. Most of QTL mapping studies were carried out from crosses made within the subspecies, either indica × indica or japonica × japonica. In this study we report advantages of using Multi-parent Advanced Generation Inter-Crosses global population, derived from a combination of eight indica and eight japonica elite parents, in QTL discovery for yield and grain quality traits. Genome-wide association study and interval mapping identified 38 and 34 QTLs whereas Bayesian networking detected 60 QTLs with 22 marker-marker associations, 32 trait-trait associations and 65 marker-trait associations. Notably, nine known QTLs/genes qPH1/OsGA20ox2, qDF3/OsMADS50, PL, QDg1, qGW-5b, grb7-2, qGL3/GS3, Amy6/Wx gene and OsNAS3 were consistently identified by all approaches for nine traits whereas qDF3/OsMADS50 was co-located for both yield and days-to-flowering traits on chromosome 3. Moreover, we identified a number of candidate QTLs in either one or two analyses but further validations will be needed. The results indicate that this new population has enabled identifications of significant QTLs and interactions for 16 traits through multiple approaches. Pyramided recombinant inbred lines provide a valuable source for integration into future breeding programs.

Genetic architecture of grain yield in bread wheat based on genome-wide association studies

BackgroundIdentification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Two genome-wide association study (GWAS) methods were used on a diverse panel of 166 elite wheat varieties from the Yellow and Huai River Valleys Wheat Zone (YHRVWD) of China to detect stable loci and analyze relationships among GY and related traits.ResultsA total of 326,570 single nucleotide polymorphism (SNP) markers from the wheat 90 K and 660 K SNP arrays were chosen for GWAS of GY and related traits, generating a physical distance of 14,064.8 Mb. One hundred and twenty common loci were detected using SNP-GWAS and Haplotype-GWAS, among which two were potentially functional genes underpinning kernel weight and plant height (PH), eight were at similar locations to the quantitative trait loci (QTL) identified in recombinant inbred line (RIL) populations in a previous study, and 78 were potentially new. Twelve pleiotropic loci were detected on eight chromosomes; among these the interval 714.4–725.8 Mb on chromosome 3A was significantly associated with GY, kernel number per spike (KNS), kernel width (KW), spike dry weight (SDW), PH, uppermost internode length (UIL), and flag leaf length (FLL). GY shared five loci with thousand kernel weight (TKW) and PH, indicating significantly affected by two traits. Compared with the total number of loci for each trait in the diverse panel, the average number of alleles for increasing phenotypic values of GY, TKW, kernel length (KL), KW, and flag leaf width (FLW) were higher, whereas the numbers for PH, UIL and FLL were lower. There were significant additive effects for each trait when favorable alleles were combined. UIL and FLL can be directly used for selecting high-yielding varieties, whereas FLW can be used to select spike number per unit area (SN) and KNS.ConclusionsThe loci and significant SNP markers identified in the present study can be used for pyramiding favorable alleles in developing high-yielding varieties. Our study proved that both GWAS methods and high-density genetic markers are reliable means of identifying loci for GY and related traits, and provided new insight to the genetic architecture of GY.

Genome-Wide Association Mapping and Genomic Prediction Analyses Reveal the Genetic Architecture of Grain Yield and Flowering Time Under Drought and Heat Stress Conditions in Maize.

Drought stress (DS) is a major constraint to maize yield production. Heat stress (HS) alone and in combination with DS are likely to become the increasing constraints. Association mapping and genomic prediction (GP) analyses were conducted in a collection of 300 tropical and subtropical maize inbred lines to reveal the genetic architecture of grain yield and flowering time under well-watered (WW), DS, HS, and combined DS and HS conditions. Out of the 381,165 genotyping-by-sequencing SNPs, 1549 SNPs were significantly associated with all the 12 trait-environment combinations, the average PVE (phenotypic variation explained) by these SNPs was 4.33%, and 541 of them had a PVE value greater than 5%. These significant associations were clustered into 446 genomic regions with a window size of 20 Mb per region, and 673 candidate genes containing the significantly associated SNPs were identified. In addition, 33 hotspots were identified for 12 trait-environment combinations and most were located on chromosomes 1 and 8. Compared with single SNP-based association mapping, the haplotype-based associated mapping detected fewer number of significant associations and candidate genes with higher PVE values. All the 688 candidate genes were enriched into 15 gene ontology terms, and 46 candidate genes showed significant differential expression under the WW and DS conditions. Association mapping results identified few overlapped significant markers and candidate genes for the same traits evaluated under different managements, indicating the genetic divergence between the individual stress tolerance and the combined drought and HS tolerance. The GP accuracies obtained from the marker-trait associated SNPs were relatively higher than those obtained from the genome-wide SNPs for most of the target traits. The genetic architecture information of the grain yield and flowering time revealed in this study, and the genomic regions identified for the different trait-environment combinations are useful in accelerating the efforts on rapid development of the stress-tolerant maize germplasm through marker-assisted selection and/or genomic selection.

Dissecting the genetics underlying the relationship between protein content and grain yield in a large hybrid wheat population.

Additive and dominance effect QTL for grain yield and protein content display antagonistic pleiotropic effects, making genomic selection based on the index grain protein deviation a promising method to alleviate the negative correlation between these traits in wheat breeding. Grain yield and quality-related traits such as protein content and sedimentation volume are key traits in wheat breeding. In this study, we used a large population of 1604 hybrids and their 135 parental components to investigate the genetics and metabolomics underlying the negative relationship of grain yield and quality, and evaluated approaches for their joint improvement. We identified a total of nine trait-associated metabolites and show that prediction using genomic data alone resulted in the highest prediction ability for all traits. We dissected the genetic architecture of grain yield and quality-determining traits and show results of the first mapping of the derived trait grain protein deviation. Further, we provide a genetic analysis of the antagonistic relation of grain yield and protein content and dissect the mode of gene action (pleiotropy vs linkage) of identified QTL. Lastly, we demonstrate that the composition of the training set for genomic prediction is crucial when considering different quality classes in wheat breeding.

Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

BackgroundIncreasing grain yield is a primary objective of maize breeding. Dissecting the genetic architecture of grain yield furthers genetic improvements to increase yield. Presented here is an association panel composed of 126 maize inbreds (AM126), which were genotyped by the genotyping-by-sequencing (tGBS) method. We performed genetic characterization and association analysis related to grain yield in the association panel.ResultsIn total, 46,046 SNPs with a minor allele frequency (MAF) ≥0.01 were used to assess genetic diversity and kinship in AM126. The results showed that the average MAF and polymorphism information content (PIC) were 0.164 and 0.198, respectively. The Shaan B group, with 11,284 unique SNPs, exhibited greater genetic diversity than did the Shaan A group, with 2644 SNPs. The 61.82% kinship coefficient in AM126 was equal to 0, and only 0.15% of that percentage was greater than 0.7. A total of 31,983 SNPs with MAF ≥0.05 were used to characterize population structure, LD decay and association mapping. Population structure analysis suggested that AM126 can be divided into 6 subgroups, which is consistent with breeding experience and pedigree information. The LD decay distance in AM126 was 150 kb. A total of 51 significant SNPs associated with grain yield were identified at P < 1 × 10− 3 across two environments (Yangling and Yulin). Among those SNPs, two loci displayed overlapping regions in the two environments. Finally, 30 candidate genes were found to be associated with grain yield.ConclusionsThese results contribute to the genetic characterization of this breeding population, which serves as a reference for hybrid breeding and population improvement, and demonstrate the genetic architecture of maize grain yield, potentially facilitating genetic improvement.

Genome-wide mapping and prediction suggests presence of local epistasis in a vast elite winter wheat populations adapted to Central Europe.

Genome-wide association mapping as well as marker- and haplotype-based genome-wide selection unraveled a complex genetic architecture of grain yield with absence of large effect QTL and presence of local epistatic effects. The genetic architecture of grain yield determines to a large extent the optimum design of genomic-assisted wheat breeding programs. The main goal of our study was to examine the potential and limitations to dissect the genetic architecture of grain yield in wheat using a large experimental data set. Our study was based on phenotypic information and genomic data of 13,901 SNPs of a diverse set of 3816 elite wheat lines adapted to Central Europe. We applied genome-wide association mapping based on experimental and simulated data sets and performed marker- and haplotype-based genomic prediction. Computer simulations revealed for our mapping population a high power to detect QTL, even if they individually explained only 2.5% of the genetic variation. Despite this, we found no stable marker-trait associations when validating in independent subsets. A two-dimensional scan for marker-marker interactions indicated presence of local epistasis which was further supported by improved prediction abilities when shifting from marker- to haplotype-based genome-wide prediction approaches. We observed that marker effects estimated using genome-wide prediction approaches strongly varied across years albeit resulting in high prediction abilities. Thus, our results suggested that the prediction accuracy of genomic selection in wheat is mainly driven by relatedness rather than by exploiting knowledge of the genetic architecture.

Assessment of Genetic Architecture of Grain Yield and its Component Traits in Barley (Hordeum vulgareL.) through Generation Mean Analysis

The suitable breeding procedure for crop improvement mainly depends on knowledge of the genetic make-up of the character to be selected. Unique architectural phenotypes have the vast potential for increasing the yield of the crop. Therefore, the investigation was carried out during three successive seasons Rabi 2009–10, 2010–11 and 2011–12 at Agriculture Research Farm, Banaras Hindu University, U.P. India with objective to estimate the main genetic effects including digenic non-allelic interactions controlling yield and yield component traits as-well-as to determine the yield component that affects yield to a greater extent. The generation mean analysis was carried out on six generations (P1, P2, F1, F2, B1 and B2) in six crosses involving two tester (LAKHAN and BH-902) and three exotic lines (MOROC-9-75, BEECHER and HARMAL) of barley. Duplicate type of epistasis was found for most of the traits in certain cross combinations, whose effect can be wiped out by following sophisticated selection procedure such as reciprocal recurrent selection and/or biparental mating in early segregating generations for the development of high yielding barley varieties with desirable yield contributing traits.