Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare

Comprehensive insights on association mapping in perennial fruit crops breeding - Its implications, current status and future perspectives

In order to provide food and nutritional security for the world's rapidly expanding population, fruit crop researchers have identified two critical priorities: increasing production and preserving fruit quality during the pre- and post-harvest periods. The genetic basis of these complex, commercially important fruit traits which are uniquely regulated by polygenes or multi-allelic genes that interact with one another and the environment can be analyzed with the aid of trait mapping tools. The most interesting trait mapping approach that offers the genetic level investigation for marker-trait associations (MTAs) for these complex fruit traits, without the development of mapping population, is association mapping. This approach was used during the genetic improvement program, emphasizing the obstacles (breeding strategies adopted, generation interval, and their genomic status) pertaining to perennial fruit crops. This method of studying population diversity and linkage disequilibrium in perennial fruit crops has been made possible by recent developments in genotyping, phenotyping, and statistical analysis. Thus, the purpose of this review is to provide an overview of different trait mapping techniques, with a focus on association mapping (method, essential components, viability, constraints, and future perspective) and its advantages, disadvantages, and possibilities for breeding perennial fruit crops.

Effective population size in field pea

BACKGROUND

Effective population size (Ne) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and the contemporary status of genetic diversity in breeding populations. The population with smaller Ne can lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance of Ne has become increasingly recognized in plant breeding, which can help breeders monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the first Ne estimates based on linkage disequilibrium (LD) in the pea genome.

RESULTS

We calculated and compared Ne using SNP markers from North Dakota State University (NDSU) modern breeding lines and United States Department of Agriculture (USDA) diversity panel. The extent of LD was highly variable not only between populations but also among different regions and chromosomes of the genome. Overall, NDSU had a higher and longer-range LD than the USDA that could extend up to 500 Kb, with a genome-wide average r2 of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated Ne for the USDA was nearly three-fold higher (Ne = 174) than NDSU (Ne = 64), which can be confounded by a high degree of population structure due to the selfing nature of pea.

CONCLUSIONS

Our results provided insights into the genetic diversity of the germplasm studied, which can guide plant breeders to actively monitor Ne in successive cycles of breeding to sustain viability of the breeding efforts in the long term.

Exploring the genetic basis of resistance to Neopestalotiopsis species in strawberry

Aggressive strains of Neopestalotiopsis sp. have recently emerged as devastating pathogens of strawberry (Fragaria × ananassa Duchesne ex Rozier), infecting nearly all plant parts and causing severe outbreaks of leaf spot and fruit rot in Florida and globally. The development of host resistance is imperative due to the absence of fungicides that effectively inhibit Neopestalotiopsis sp. growth on an infected strawberry crop. Here, we analyzed 1578 individuals from the University of Florida's (UF) strawberry breeding program to identify and dissect genetic variation for resistance to Neopestalotiopsis sp. and to explore the feasibility of genomic selection. We found that less than 12% of elite UF germplasm exhibited resistance, with narrow-sense heritability estimates ranging from 0.28 to 0.69. Through genome-wide association studies (GWAS), we identified two loci accounting for 7%-16% of phenotypic variance across four trials and 3 years. Several candidate genes encoding pattern recognition receptors, intra-cellular nucleotide-binding leucine-rich repeats, and downstream components of plant defense pathways co-localized with the Neopestalotiopsis sp. resistance loci. Interestingly, favorable alleles at the largest-effect locus were rare in elite UF material and had previously been unintentionally introduced from an exotic cultivar. The array-based markers and candidate genes described herein provide the foundation for targeting this locus through marker-assisted selection. The predictive abilities of genomic selection models, with and without explicitly modeling peak GWAS markers as fixed effects, ranged between 0.25 and 0.59, suggesting that genomic selection holds promise for enhancing resistance to Neopestalotiopsis sp. in strawberry.

Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT)

In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. Northern European barley germplasm has been relatively understudied despite its key role within the malting industry. The European Heritage Barley collection (ExHIBiT) was assembled to explore the genetic diversity in European barley focusing on Northern European accessions and further address environmental pressures. ExHIBiT consists of 363 spring-barley accessions, focusing on two-row type. The collection consists of landraces (~14%), old cultivars (~18%), elite cultivars (~67%) and accessions with unknown breeding history (~1%), with 70% of the collection from Northern Europe. The population structure of the ExHIBiT collection was subdivided into three main clusters primarily based on the accession's year of release using 26,585 informative SNPs based on 50k iSelect single nucleotide polymorphism (SNP) array data. Power analysis established a representative core collection of 230 genotypically and phenotypically diverse accessions. The effectiveness of this core collection for conducting statistical and association analysis was explored by undertaking genome-wide association studies (GWAS) using 24,876 SNPs for nine phenotypic traits, four of which were associated with SNPs. Genomic regions overlapping with previously characterised flowering genes (HvZTLb) were identified, demonstrating the utility of the ExHIBiT core collection for locating genetic regions that determine important traits. Overall, the ExHIBiT core collection represents the high level of untapped diversity within Northern European barley, providing a powerful resource for researchers and breeders to address future climate scenarios.

UDP-glucosyltransferase HvUGT13248 confers type II resistance to Fusarium graminearum in barley

Fusarium head blight (FHB) of barley (Hordeum vulgare) causes yield losses and accumulation of trichothecene mycotoxins (e.g. deoxynivalenol [DON]) in grains. Glucosylation of DON to the nontoxic DON-3-O-glucoside (D3G) is catalyzed by UDP-glucosyltransferases (UGTs), such as barley UGT13248. We explored the natural diversity of UGT13248 in 496 barley accessions and showed that all carried potential functional alleles of UGT13248, as no genotypes showed strongly increased seedling sensitivity to DON. From a TILLING population, we identified 2 mutant alleles (T368I and H369Y) that, based on protein modeling, likely affect the UDP-glucose binding of UGT13248. In DON feeding experiments, DON-to-D3G conversion was strongly reduced in spikes of these mutants compared to controls, and plants overexpressing UGT13248 showed increased resistance to DON and increased DON-to-D3G conversion. Moreover, field-grown plants carrying the T368I or H369Y mutations inoculated with Fusarium graminearum showed increased FHB disease severity and reduced D3G production. Barley is generally considered to have type II resistance that limits the spread of F. graminearum from the infected spikelet to adjacent spikelets. Point inoculation experiments with F. graminearum showed increased infection spread in T368I and H369Y across the spike compared to wild type, while overexpression plants showed decreased spread of FHB symptoms. Confocal microscopy revealed that F. graminearum spread to distant rachis nodes in T368I and H369Y mutants but was arrested at the rachis node of the inoculated spikelet in wild-type plants. Taken together, our data reveal that UGT13248 confers type II resistance to FHB in barley via conjugation of DON to D3G.

Genome wide association analysis for grain micronutrients and anti-nutritional traits in mungbean [Vigna radiata (L.) R. Wilczek] using SNP markers

Mungbean is an important food grain legume for human nutrition and nutritional food due to its nutrient-dense seed, liked palatability, and high digestibility. However, anti-nutritional factors pose a significant risk to improving nutritional quality for bio-fortification. In the present study, genetic architecture of grain micronutrients (grain iron and zinc concentration) and anti-nutritional factors (grain phytic acid and tannin content) in association mapping panel of 145 diverse mungbean were evaluated. Based on all four parameters genotypes PUSA 1333 and IPM 02-19 were observed as desired genotypes as they had high grain iron and zinc concentration but low grain phytic acid and tannin content. The next generation sequencing (NGS)-based genotyping by sequencing (GBS) identified 14,447 genome-wide SNPs in a diverse selected panel of 127 mungbean genotypes. Population admixture analysis revealed the presence of four different ancestries among the genotypes and LD decay of ∼57.6 kb kb physical distance was noted in mungbean chromosomes. Association mapping analysis revealed that a total of 20 significant SNPs were shared by both GLM and Blink models associated with grain micronutrient and anti-nutritional factor traits, with Blink model identifying 35 putative SNPs. Further, this study identified the 185 putative candidate genes. Including potential candidate genes Vradi07g30190, Vradi01g09630, and Vradi09g05450 were found to be associated with grain iron concentration, Vradi10g04830 with grain zinc concentration, Vradi08g09870 and Vradi01g11110 with grain phytic acid content and Vradi04g11580 and Vradi06g15090 with grain tannin content. Moreover, two genes Vradi07g15310 and Vradi09g05480 showed significant variation in protein structure between native and mutated versions. The identified SNPs and candidate genes are potential powerful tools to provide the essential information for genetic studies and marker-assisted breeding program for nutritional improvement in mungbean.

Novel Hina alleles created by genome editing increase grain hardness and reduce grain width in barley

The hordoindolina genes (Hina and Hinb) are believed to play critical roles in barley (Hordeum vulgare L.) grain texture. In this study, we created novel alleles of the Hina gene using CRISPR/Cas9 (Clustered regularly inter spaced short palindromic repeat-associated protein, CRISPR-Cas) genome editing. Mutagenesis of single bases in these novel alleles led to loss of Hina protein function in edited lines. The grain hardness index of hina mutants was 95.5 on average, while that of the wild type was only 53.7, indicating successful conversion of soft barley into hard barley. Observation of cross-sectional grain structure using scanning electron microscopy revealed different adhesion levels between starch granules and protein matrix. Starch granules were loose and separated from the protein matrix in the wild type, but deeply trapped and tightly integrated with the protein matrix in hina02 mutants. In addition, the grain width and thousand-grain weight of the hina02 mutant were significantly lower than those of the wild type.

Identification of New QTLs for Dietary Fiber Content in Aegilops biuncialis

Grain dietary fiber content is an important health-promoting trait of bread wheat. A dominant dietary fiber component of wheat is the cell wall polysaccharide arabinoxylan and the goatgrass Aegilops biuncialis has high β-glucan content, which makes it an attractive gene source to develop wheat lines with modified fiber composition. In order to support introgression breeding, this work examined genetic variability in grain β-glucan, pentosan, and protein content in a collection of Ae. biuncialis. A large variation in grain protein and edible fiber content was revealed, reflecting the origin of Ae. biuncialis accessions from different eco-geographical habitats. Association analysis using DArTseq-derived SNPs identified 34 QTLs associated with β-glucan, pentosan, water-extractable pentosan, and protein content. Mapping the markers to draft chromosome assemblies of diploid progenitors of Ae. biuncialis underlined the role of genes on chromosomes 1M^b, 4M^b, and 5M^b in the formation of grain β-glucan content, while other QTLs on chromosome groups 3, 6, and 1 identified genes responsible for total- and water-extractable pentosan content. Functional annotation of the associated marker sequences identified fourteen genes, nine of which were identified in other monocots. The QTLs and genes identified in the present work are attractive targets for chromosome-mediated gene transfer to improve the health-promoting properties of wheat-derived foods.

Physical geography, isolation by distance and environmental variables shape genomic variation of wild barley (Hordeum vulgare L. ssp. spontaneum) in the Southern Levant

Determining the extent of genetic variation that reflects local adaptation in crop-wild relatives is of interest for the purpose of identifying useful genetic diversity for plant breeding. We investigated the association of genomic variation with geographical and environmental factors in wild barley (Hordeum vulgare L. ssp. spontaneum) populations of the Southern Levant using genotyping by sequencing (GBS) of 244 accessions in the Barley 1K+ collection. The inference of population structure resulted in four genetic clusters that corresponded to eco-geographical habitats and a significant association between lower gene flow rates and geographical barriers, e.g. the Judaean Mountains and the Sea of Galilee. Redundancy analysis (RDA) revealed that spatial autocorrelation explained 45% and environmental variables explained 15% of total genomic variation. Only 4.5% of genomic variation was solely attributed to environmental variation if the component confounded with spatial autocorrelation was excluded. A synthetic environmental variable combining latitude, solar radiation, and accumulated precipitation explained the highest proportion of genomic variation (3.9%). When conditioned on population structure, soil water capacity was the most important environmental variable explaining 1.18% of genomic variation. Genome scans with outlier analysis and genome-environment association studies were conducted to identify adaptation signatures. RDA and outlier methods jointly detected selection signatures in the pericentromeric regions, which have reduced recombination, of the chromosomes 3H, 4H, and 5H. However, selection signatures mostly disappeared after correction for population structure. In conclusion, adaptation to the highly diverse environments of the Southern Levant over short geographical ranges had a limited effect on the genomic diversity of wild barley. This highlighted the importance of nonselective forces in genetic differentiation.

Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad-spectrum resistance

Powdery mildew isa major disease of barley (Hordeum vulgare L.) for which breeders have traditionally relied on dominant, pathogen race-specific resistance genes for genetic control. Directional selection pressures in extensive monocultures invariably result in such genes being overcome as the pathogen mutates to evade recognition. This has led to a widespread reliance on fungicides and a single broad-spectrum recessive resistance provided by the mlo gene. The range of resistance genes and alleles found in wild crop relatives and landraces has been reduced in agricultural cultivars through an erosion of genetic diversity during domestication and selective breeding. Three novel major-effect adult plant resistance (APR) genes from landraces, designated Resistance to Blumeria graminis f. sp. hordei (Rbgh1 to Rbgh3), were identified in the terminal regions of barley chromosomes 5HL, 7HS, and 1HS, respectively. The phenotype of the new APR genes showed neither pronounced penetration resistance, nor the spontaneous necrosis and mesophyll cell death typical of mlo resistance, nor a whole epidermal cell hypersensitive response, typical of race-specific resistance. Instead, resistance was localized to the site of attempted penetration in an epidermal cell and was associated with cell wall appositions and cytosolic vesicle-like bodies, and lacked strong induction of reactive oxygen species. The APR genes exhibited differences in vesicle-like body sizes, their distribution, and the extent of localized 3,3-diaminobenzidine staining in individual doubled haploid lines. The results revealed a set of unique basal penetration resistance genes that offer opportunities for combining different resistance mechanisms in breeding programs for robust mildew resistance.

Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel

Trehalose 6‐phosphate (T6P) signalling regulates carbon use and allocation and is a target to improve crop yields. However, the specific contributions of trehalose phosphate synthase (TPS) and trehalose phosphate phosphatase (TPP) genes to source‐ and sink‐related traits remain largely unknown. We used enrichment capture sequencing on TPS and TPP genes to estimate and partition the genetic variation of yield‐related traits in a spring wheat (Triticum aestivum) breeding panel specifically built to capture the diversity across the 75,000 CIMMYT wheat cultivar collection. Twelve phenotypes were correlated to variation in TPS and TPP genes including plant height and biomass (source), spikelets per spike, spike growth and grain filling traits (sink) which showed indications of both positive and negative gene selection. Individual genes explained proportions of heritability for biomass and grain‐related traits. Three TPS1 homologues were particularly significant for trait variation. Epistatic interactions were found within and between the TPS and TPP gene families for both plant height and grain‐related traits. Gene‐based prediction improved predictive ability for grain weight when gene effects were combined with the whole‐genome markers. Our study has generated a wealth of information on natural variation of TPS and TPP genes related to yield potential which confirms the role for T6P in resource allocation and in affecting traits such as grain number and size confirming other studies which now opens up the possibility of harnessing natural genetic variation more widely to better understand the contribution of native genes to yield traits for incorporation into breeding programmes.

Genetic Dissection of Grain Yield Component Traits Under High Nighttime Temperature Stress in a Rice Diversity Panel

To dissect the genetic complexity of rice grain yield (GY) and quality in response to heat stress at the reproductive stage, a diverse panel of 190 rice accessions in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) diversity panel were treated with high nighttime temperature (HNT) stress at the reproductive stage of panicle initiation. The quantifiable yield component response traits were then measured. The traits, panicle length (PL), and number of spikelets per panicle (NSP) were evaluated in subsets of the panel comprising the rice subspecies Oryza sativa ssp. Indica and ssp. Japonica. Under HNT stress, the Japonica ssp. exhibited lower reductions in PL and NSP and a higher level of genetic variation compared with the other subpopulations. Whole genome sequencing identified 6.5 million single nucleotide polymorphisms (SNPs) that were used for the genome-wide association studies (GWASs) of the PL and NSP traits. The GWAS analysis in the Combined, Indica, and Japonica populations under HNT stress identified 83, 60, and 803 highly significant SNPs associated with PL, compared to the 30, 30, and 11 highly significant SNPs associated with NSP. Among these trait-associated SNPs, 140 were coincident with genomic regions previously reported for major GY component quantitative trait loci (QTLs) under heat stress. Using extents of linkage disequilibrium in the rice populations, Venn diagram analysis showed that the highest number of putative candidate genes were identified in the Japonica population, with 20 putative candidate genes being common in the Combined, Indica and Japonica populations. Network analysis of the genes linked to significant SNPs associated with PL and NSP identified modules that were involved in primary and secondary metabolisms. The findings in this study could be useful to understand the pathways/mechanisms involved in rice GY and its components under HNT stress for the acceleration of rice-breeding programs and further functional analysis by molecular geneticists.

Association analysis of physiological traits in spring barley (Hordeum vulgare L.) under water-deficit conditions

In the present study, 148 commercial barley cultivars were assessed by 14 AFLP primer combinations and 32 SSRs primer pairs. Population structure, linkage disequilibrium, and genomic regions associated with physiological traits under drought stress were investigated. The phenotypic results showed a high level of diversity between studied cultivars. The studied barley cultivars were divided into two subgroups. Linkage disequilibrium analysis revealed that r 2 values among all possible marker pairs have an average value of 0.0178. The mixed linear model procedure showed that totally, 207 loci had a significant association with investigated traits. 120 QTLs out of 207 were detected for traits under normal conditions, and 90 QTLs were detected for traits under drought stress conditions. Identified QTLs after validation and transferring to SCAR markers in the case of AFLPs can be used to develop MAS strategies for barley breeding programs. Some common markers were identified for a particular trait or some traits across normal and drought stress conditions. These markers show low interaction with environmental conditions (stable markers); therefore, selection by them for a trait under normal conditions will improve the trait value under stress conditions, too.

The influence of breeding history, origin and growth type on population structure of barley as revealed by SSR markers

Natural and mass selection during domestication and cultivation favored particular traits of interest in barley. In the present study, population structure, and genetic relationships among 144 accessions of barley landraces and breeding materials from various countries were studied using a set of 77 and 72 EST-SSR and gSSR markers, respectively distributed on seven chromosomes of barley. In total, 262 and 429 alleles were amplified in 77 EST-SSRs and 72 gSSR loci, respectively. Out of which, 185 private/group-specific alleles were identified in the landraces compared with 14 in "cultivar and advanced breeding lines", indicating the possibility to introgress favorite alleles from landraces into breeding materials. Comparative analysis of genetic variation among breeding materials, Iranian landraces, and exotic landraces revealed higher genetic diversity in Iranian landraces compared with others. A total of 37, 15, and 14 private/group-specific alleles were identified in Iranian landraces, exotic landraces, and breeding materials, respectively. The most likely groups for 144 barley genotypes were three as inferred using model- and distance-based clustering as well as principal coordinate analysis which assigned the landraces and breeding materials into separate groups. The distribution of alleles was found to be correlated with population structure, domestication history and eco-geographical factors. The high allelic richness in the studied set of barley genotype provides insights into the available diversity and allows the construction of core groups based on maximizing allelic diversity for use in barley breeding programs.

Genome-wide association analysis of natural variation in seed tocochromanols of barley

Tocochromanols (tocols for short), commonly called Vitamin E, are lipid-soluble plant antioxidants vital for regulating lipid peroxidation in chloroplasts and seeds. Barley (Hordeum vulgare L.) seeds contain all eight different isoforms of tocols; however, the extent of natural variation in their composition and their underlying genetic basis is not known. Tocol levels in barley seeds were quantified in diverse H. vulgare panels comprising 297 wild lines from a diversity panel and 160 cultivated spring-type accessions from the mini-core panel representing the genetic diversity of the USDA barley germplasm collection. Significant differences were observed in the concentration of tocols between the two panels. To identify the genes associated with tocols, genome-wide association analysis was conducted with single nucleotide polymorphisms (SNPs) from Illumina arrays for the mini-core panel and genotyping-by-sequencing for the wild barley panel. Forty unique SNPs in the wild barley and 27 SNPs in the mini-core panel were significantly associated with various tocols. Marker-trait associations (MTAs) were identified on chromosomes 1, 6, and 7 for key genes in the tocol biosynthesis pathway, which have also been reported in other studies. Several novel MTAs were identified on chromosomes 2, 3, 4 and 5 and were found to be in proximity to genes involved in the generation of precursor metabolites required for tocol biosynthesis. This study provides a valuable resource for barley breeding programs targeting specific isoforms of seed tocols and for investigating the physiological roles of these metabolites in seed longevity, dormancy, and germination.

Identification, Association of Natural Variation and Expression Analysis of ZmNAC9 Gene Response to Low Phosphorus in Maize Seedling Stage

Phosphorus (P) is an essential macroelement supporting maize productivity and low-P stress is a limiting factor of maize growth and yield. Improving maize plant tolerance to low P through molecular breeding is an effective alternative to increase crop productivity. In this study, a total of 111 diverse maize inbred lines were used to identify the favorable alleles and nucleotide diversity of candidate ZmNAC9, which plays an important role in response to low P and regulation in root architecture. A significant difference was found under low- and sufficient-P conditions for each of the 22 seedling traits, and a total of 41 polymorphic sites including 32 single nucleotide polymorphisms (SNPs) and 9 insertion and deletions (InDels) were detected in ZmNAC9 among 111 inbred lines. Among the 41 polymorphic studied sites, a total of 39 polymorphic sites were associated with 20 traits except for the dry weight of shoots and forks, of which six sites were highly significantly associated with a diverse number of low-P tolerant root trait index values by using a mixed linear model (MLM) at −log10 P = 3.61. In addition, 29 polymorphic sites under P-sufficient and 32 polymorphic sites under P-deficient conditions were significantly associated with a diverse number of seedling traits, of which five polymorphic sites (position S327, S513, S514, S520, and S827) were strongly significantly associated with multiple seedling traits under low-P and normal-P conditions. Among highly significant sites, most of the sites were associated with root traits under low-P, normal-P, and low-P trait index values. Linkage disequilibrium (LD) was strong at (r2 > 1.0) in 111 inbred lines. Furthermore, the effect of five significant sites was verified for haplotypes in 111 lines and the favorable allele S520 showed a positive effect on the dry weight of roots under the low-P condition. Furthermore, the expression pattern confirmed that ZmNAC9 was highly induced by low P in the roots of the P-tolerant 178 inbred line. Moreover, the subcellular localization of ZmNAC9 encoded by protein was located in the cytoplasm and nucleus. Haplotypes carrying more favorable alleles exhibited superior effects on phenotypic variation and could be helpful in developing molecular markers in maize molecular breeding programs. Taken together, the finding of this study might lead to further functions of ZmNAC9 and genes that might be involved in responses to low-P stress in maize.

Dissecting new genetic components of salinity tolerance in two-row spring barley at the vegetative and reproductive stages

Soil salinity imposes an agricultural and economic burden that may be alleviated by identifying the components of salinity tolerance in barley, a major crop and the most salt tolerant cereal. To improve our understanding of these components, we evaluated a diversity panel of 377 two-row spring barley cultivars during both the vegetative, in a controlled environment, and the reproductive stages, in the field. In the controlled environment, a high-throughput phenotyping platform was used to assess the growth-related traits under both control and saline conditions. In the field, the agronomic traits were measured from plots irrigated with either fresh or saline water. Association mapping for the different components of salinity tolerance enabled us to detect previously known associations, such as HvHKT1;5. Using an "interaction model", which took into account the interaction between treatment (control and salt) and genetic markers, we identified several loci associated with yield components related to salinity tolerance. We also observed that the two developmental stages did not share genetic regions associated with the components of salinity tolerance, suggesting that different mechanisms play distinct roles throughout the barley life cycle. Our association analysis revealed that genetically defined regions containing known flowering genes (Vrn-H3, Vrn-H1, and HvNAM-1) were responsive to salt stress. We identified a salt-responsive locus (7H, 128.35 cM) that was associated with grain number per ear, and suggest a gene encoding a vacuolar H+-translocating pyrophosphatase, HVP1, as a candidate. We also found a new QTL on chromosome 3H (139.22 cM), which was significant for ear number per plant, and a locus on chromosome 2H (141.87 cM), previously identified using a nested association mapping population, which associated with a yield component and interacted with salinity stress. Our study is the first to evaluate a barley diversity panel for salinity stress under both controlled and field conditions, allowing us to identify contributions from new components of salinity tolerance which could be used for marker-assisted selection when breeding for marginal and saline regions.

GWAS: Fast-forwarding gene identification and characterization in temperate Cereals: lessons from Barley - A review

Understanding the genetic complexity of traits is an important objective of small grain temperate cereals yield and adaptation improvements. Bi-parental quantitative trait loci (QTL) linkage mapping is a powerful method to identify genetic regions that co-segregate in the trait of interest within the research population. However, recently, association or linkage disequilibrium (LD) mapping using a genome-wide association study (GWAS) became an approach for unraveling the molecular genetic basis underlying the natural phenotypic variation. Many causative allele(s)/loci have been identified using the power of this approach which had not been detected in QTL mapping populations. In barley (Hordeum vulgare L.), GWAS has been successfully applied to define the causative allele(s)/loci which can be used in the breeding crop for adaptation and yield improvement. This promising approach represents a tremendous step forward in genetic analysis and undoubtedly proved it is a valuable tool in the identification of candidate genes. In this review, we describe the recently used approach for genetic analyses (linkage mapping or association mapping), and then provide the basic genetic and statistical concepts of GWAS, and subsequently highlight the genetic discoveries using GWAS. The review explained how the candidate gene(s) can be detected using state-of-art bioinformatic tools.

The Fate of Deleterious Variants in a Barley Genomic Prediction Population

Targeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a "cost of domestication." This includes an increase in the proportion of genetic variants that are likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley lines, we identified 3855 dSNPs among 497,754 total SNPs. We generated whole-genome resequencing data of Hordeum murinum ssp. glaucum as a phylogenetic outgroup to polarize SNPs as ancestral vs. derived. We also observed a higher proportion of dSNPs per synonymous SNPs (sSNPs) in low-recombination regions of the genome. Using 5215 progeny from a genomic prediction experiment, we examined the fate of dSNPs over three breeding cycles. Adjusting for initial frequency, derived alleles at dSNPs reduced in frequency or were lost more often than other classes of SNPs. The highest-yielding lines in the experiment, as chosen by standard genomic prediction approaches, carried fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction had a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.

Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target-capture method was used to detect genome-wide polymorphisms in a panel of 174 flowering time-related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas.

Evaluation of RR-BLUP Genomic Selection Models that Incorporate Peak Genome-Wide Association Study Signals in Maize and Sorghum

Certain agronomic crop traits are complex and thus governed by many small-effect loci. Statistical models typically used in a genome-wide association study (GWAS) and genomic selection (GS) quantify these signals by assessing genomic marker contributions in linkage disequilibrium (LD) with these loci to trait variation. These models have been used in separate quantitative genetics contexts until recently, when, in published studies, the predictive ability of GS models that include peak associated markers from a GWAS as fixed-effect covariates was assessed. Previous work suggests that such models could be useful for predicting traits controlled by several large-effect and many small-effect genes. We expand this work by evaluating simulated traits from diversity panels in maize ( L.) and sorghum [ (L.) Moench] using ridge-regression best linear unbiased prediction (RR-BLUP) models that include fixed-effect covariates tagging peak GWAS signals. The ability of such covariates to increase GS prediction accuracy in the RR-BLUP model under a wide variety of genetic architectures and genomic backgrounds was quantified. Of the 216 genetic architectures that we simulated, we identified 60 where the addition of fixed-effect covariates boosted prediction accuracy. However, for the majority of the simulated data, no increase or a decrease in prediction accuracy was observed. We also noted several instances where the inclusion of fixed-effect covariates increased both the variability of prediction accuracies and the bias of the genomic estimated breeding values. We therefore recommend that the performance of such a GS model be explored on a trait-by-trait basis prior to its implementation into a breeding program.

Usefulness of a Multiparent Advanced Generation Intercross Population With a Greatly Reduced Mating Design for Genetic Studies in Winter Wheat

Multiparent advanced generation intercross (MAGIC) populations were recently developed to allow the high-resolution mapping of quantitative traits. We present a genetic linkage map of an elite but highly diverse eight-founder MAGIC population in common wheat (Triticum aestivum L.). Our MAGIC population is composed of 394 F6:8 recombinant inbred lines lacking significant signatures of population structure. The linkage map included 5435 SNP markers distributed over 2804 loci and spanning 5230 cM. The analysis of population parameters, including genetic structure, kinship, founder probabilities, and linkage disequilibrium and congruency to other maps indicated appropriate construction of both the population and the genetic map. It was shown that eight-founder MAGIC populations exhibit a greater number of loci and higher recombination rates, especially in the pericentromeric regions, compared to four-founder MAGIC, and biparental populations. In addition, our greatly simplified eight-parental MAGIC mating design with an additional eight-way intercross step was found to be equivalent to a MAGIC design with all 210 possible four-way crosses regarding the levels of missing founder assignments and the number of recombination events. Furthermore, the MAGIC population captured 71.7% of the allelic diversity available in the German wheat breeding gene pool. As a proof of principle, we demonstrated the application of the resource for quantitative trait loci mapping analyzing seedling resistance to powdery mildew. As wheat is a crop with many breeding objectives, this resource will allow scientists and breeders to carry out genetic studies for a wide range of breeder-relevant parameters in a single genetic background and reveal possible interactions between traits of economic importance.

Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize

Genome-wide association studies (GWAS) have identified loci linked to hundreds of traits in many different species. Yet, because linkage equilibrium implicates a broad region surrounding each identified locus, the causal genes often remain unknown. This problem is especially pronounced in nonhuman, nonmodel species, where functional annotations are sparse and there is frequently little information available for prioritizing candidate genes. We developed a computational approach, Camoco, that integrates loci identified by GWAS with functional information derived from gene coexpression networks. Using Camoco, we prioritized candidate genes from a large-scale GWAS examining the accumulation of 17 different elements in maize (Zea mays) seeds. Strikingly, we observed a strong dependence in the performance of our approach based on the type of coexpression network used: expression variation across genetically diverse individuals in a relevant tissue context (in our case, roots that are the primary elemental uptake and delivery system) outperformed other alternative networks. Two candidate genes identified by our approach were validated using mutants. Our study demonstrates that coexpression networks provide a powerful basis for prioritizing candidate causal genes from GWAS loci but suggests that the success of such strategies can highly depend on the gene expression data context. Both the software and the lessons on integrating GWAS data with coexpression networks generalize to species beyond maize.

Genotyping-by-sequencing highlights patterns of genetic structure and domestication in artichoke and cardoon

Exploiting the biodiversity of crops and their wild relatives is fundamental for maintaining and increasing food security. The species Cynara cardunculus includes three taxa: the globe artichoke, one of the most important Mediterranean vegetables, the leafy cardoon, and the wild cardoon. In this study, genotyping by sequencing (GBS) was successfully applied to reveal thousands of polymorphisms in a C. cardunculus germplasm collection, including 65 globe artichoke, 9 leafy cardoon, and 21 wild cardoon samples. The collection showed a strong population structure at K = 2, separating the globe artichoke from the leafy and wild cardoon. At higher K values, further substructures were observed, in which the wild cardoon was separated from the leafy cardoon, and the latter included the Spanish wild cardoons, while the wild sample from Portugal was admixed. Moreover, subpopulations within the globe artichoke set were highlighted. Structure analysis restricted to the globe artichoke dataset pointed out genetic differentiation between the ˝Catanesi˝ typology and all the other samples (K = 2). At higher values of K, the separation of the ˝Catanesi˝ group still held true, and green headed landraces from Apulia region, Italy (˝Green Apulian˝) formed a distinct subpopulation. ˝Romaneschi˝ artichoke types fell in a variable group with admixed samples, indicating that they should not be considered as a genetically uniform typology. The results of principal component analysis and Neighbor-Joining hierarchical clustering were consistent with structure results, and in addition provided a measure of genetic relationships among individual genotypes. Both analyses attributed the wild material from Spain and Portugal to the cultivated cardoon group, supporting the idea that this might be indeed a feral form of the leafy cardoon. Different reproductive habit and possibly selective pressure led to a slower LD decay in artichoke compared to cardoon. Genotyping by sequencing has proven a reliable methodology to obtain valuable SNPs and assess population genetics in C. cardunculus.

GWAS analysis in spring barley (Hordeum vulgare L.) for morphological traits exposed to drought

Association analysis based on linkage disequilibrium has become a common and powerful approach for detection of QTLs underlying complex agronomic traits including drought tolerance. To determine marker/trait association, 148 modern European spring barley cultivars were evaluated under drought stress. Associations of morphological traits with AFLP/SSR markers were investigated based on the mixed linear model using the TASSEL_3.0. Population structure was estimated using various methods including Bayesian clustering model by STRUCTURE software, PCoA analysis, NJ dendrogram and Hierarchical Clustering. Linkage disequilibrium patterns were explored among the whole genome and each chromosome separately. All the analysis for population structure divided the population into two sub-groups. Linkage disequilibrium analysis showed that by increasing genetic distance, LD decreases. Totally, 167 significant marker trait associations were found which delineated into 65 QTLs in both treatments. Two stable QTLs on 5H at 86.880 cM were detected for Internode Length and on 3H at 126.421 cM for flag leaf length in drought stress treatment. Fourteen QTLs were co-localized with previously reported QTLs and others were novel. The results indicate that these putative genomic regions contain genes that have pleiotropic effects on morphological traits in drought condition.

When less can be better: How can we make genomic selection more cost-effective and accurate in barley?

We were able to obtain good prediction accuracy in genomic selection with ~ 2000 GBS-derived SNPs. SNPs in genic regions did not improve prediction accuracy compared to SNPs in intergenic regions. Since genotyping can represent an important cost in genomic selection, it is important to minimize it without compromising the accuracy of predictions. The objectives of the present study were to explore how a decrease in the unit cost of genotyping impacted: (1) the number of single nucleotide polymorphism (SNP) markers; (2) the accuracy of the resulting genotypic data; (3) the extent of coverage on both physical and genetic maps; and (4) the prediction accuracy (PA) for six important traits in barley. Variations on the genotyping by sequencing protocol were used to generate 16 SNP sets ranging from ~ 500 to ~ 35,000 SNPs. The accuracy of SNP genotypes fluctuated between 95 and 99%. Marker distribution on the physical map was highly skewed toward the terminal regions, whereas a fairly uniform coverage of the genetic map was achieved with all but the smallest set of SNPs. We estimated the PA using three statistical models capturing (or not) the epistatic effect; the one modeling both additivity and epistasis was selected as the best model. The PA obtained with the different SNP sets was measured and found to remain stable, except with the smallest set, where a significant decrease was observed. Finally, we examined if the localization of SNP loci (genic vs. intergenic) affected the PA. No gain in PA was observed using SNPs located in genic regions. In summary, we found that there is considerable scope for decreasing the cost of genotyping in barley (to capture ~ 2000 SNPs) without loss of PA.

A Novel QTL for Powdery Mildew Resistance in Nordic Spring Barley (Hordeum vulgare L. ssp. vulgare) Revealed by Genome-Wide Association Study

The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley (Hordeum vulgare L. ssp. vulgare) production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012-2014) in four different locations within the Nordic region. There were strong correlations between data from all locations and years. In total four QTLs were identified, one located on chromosome 4H in the same region as the previously identified mlo locus and three on chromosome 6H. Out of these three QTLs identified on chromosome 6H, two are in the same region as previously reported QTLs for powdery mildew resistance, whereas one QTL appears to be novel. The top NCBI BLASTn hit of the SNP markers within the novel QTL predicted the responsible gene to be the 26S proteasome regulatory subunit, RPN1, which is required for innate immunity and powdery mildew-induced cell death in Arabidopsis. The results from this study have revealed SNP marker candidates that can be exploited for use in marker-assisted selection and stacking of genes for powdery mildew resistance in barley.

Genome-Wide Association Mapping of Stem Rust Resistance in Hordeum vulgare subsp. spontaneum

Stem rust was one of the most devastating diseases of barley in North America. Through the deployment of cultivars with the resistance gene Rpg1, losses to stem rust have been minimal over the past 70 yr. However, there exist both domestic (QCCJB) and foreign (TTKSK aka isolate Ug99) pathotypes with virulence for this important gene. To identify new sources of stem rust resistance for barley, we evaluated the Wild Barley Diversity Collection (WBDC) (314 ecogeographically diverse accessions of Hordeum vulgare subsp. spontaneum) for seedling resistance to four pathotypes (TTKSK, QCCJB, MCCFC, and HKHJC) of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici, Pgt) and one isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis, Pgs). Based on a coefficient of infection, the frequency of resistance in the WBDC was low ranging from 0.6% with HKHJC to 19.4% with 92-MN-90. None of the accessions was resistant to all five cultures of P. graminis A genome-wide association study (GWAS) was conducted to map stem rust resistance loci using 50,842 single-nucleotide polymorphic markers generated by genotype-by-sequencing and ordered using the new barley reference genome assembly. After proper accounting for genetic relatedness and structure among accessions, 45 quantitative trait loci were identified for resistance to P. graminis across all seven barley chromosomes. Three novel loci associated with resistance to TTKSK, QCCJB, MCCFC, and 92-MN-90 were identified on chromosomes 5H and 7H, and two novel loci associated with resistance to HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley.

Identification of quantitative trait loci associated with resistance to net form net blotch in a collection of Nordic barley germplasm

Association mapping of resistance to Pyrenophora teres f. teres in a collection of Nordic barley germplasm at different developmental stages revealed 13 quantitative loci with mostly small effects. Net blotch, caused by the necrotrophic fungus Pyrenophora teres, is one of the major diseases in barley in Norway causing quantitative and qualitative yield losses. Resistance in Norwegian cultivars and germplasm is generally insufficient and resistance sources have not been extensively explored yet. In this study, we mapped quantitative trait loci (QTL) associated with resistance to net blotch in Nordic germplasm. We evaluated a collection of 209 mostly Nordic spring barley lines for reactions to net form net blotch (NFNB; Pyrenophora teres f. teres) in inoculations with three single conidia isolates at the seedling stage and in inoculated field trials at the adult stage in 4 years. Using 5669 SNP markers genotyped with the Illumina iSelect 9k Barley SNP Chip and a mixed linear model accounting for population structure and kinship, we found a total of 35 significant marker-trait associations for net blotch resistance, corresponding to 13 QTL, on all chromosomes. Out of these QTL, seven conferred resistance only in adult plants and four were only detectable in seedlings. Two QTL on chromosomes 3H and 6H were significant during both seedling inoculations and adult stage field trials. These are promising candidates for breeding programs using marker-assisted selection strategies. The results elucidate the genetic background of NFNB resistance in Nordic germplasm and suggest that NB resistance is conferred by a number of genes each with small-to-moderate effects, making it necessary to pyramid these genes to achieve sufficient levels of resistance.

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

Demographic modelling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinct Brassica rapa crops to corroborate demographic models of domestication. Brassica rapa crops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remain unclear. We generated genomewide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across the B. rapa genome revealed evidence for five distinct genetic groups and supported a European-Central Asian origin of B. rapa crops. Our results supported the traditionally recognized South Asian and East Asian B. rapa groups with evidence that pak choi, Chinese cabbage and yellow sarson are likely monophyletic groups. In contrast, the oil-type B. rapa subsp. oleifera and brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies of B. rapa. Demographic analyses suggested that B. rapa was introduced to Asia 2,400-4,100 years ago, and that Chinese cabbage originated 1,200-2,100 years ago via admixture of pak choi and European-Central Asian B. rapa. We also inferred significantly different levels of founder effect among the B. rapa subspecies. Written records from antiquity that document these crops are consistent with these inferences. The concordance between our age estimates of domestication events with historical records provides unique support for our demographic inferences.

New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype

Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies. These strategies are complementary in most instances, and indeed, one is often used to confirm the results of the other. Despite significant advances, an emerging trend is that the outcome and efficiency of the different approaches depend greatly on the genetic architecture of the trait in the genetic material under study.

Patterns of Evolutionary Trajectories and Domestication History within the Genus Hordeum Assessed by REMAP Markers

The patterns of genetic diversity related to the taxonomy and domestication history of 85 accessions representing the main four species of the genus Hordeum were examined by retrotransposon-microsatellite amplified polymorphism (REMAP) markers based on the retrotransposon BARE-1. A substantial level of genetic polymorphisms at among- and within-species level was observed showing that this retrotransposon family and its adjacent genomic regions has been a target for genome dynamics during the evolution and domestication of barley. The obtained data are consistent with the current taxonomic status within the genus Hordeum. Similar level of genetic diversity was observed between the wild and the domesticated barley accessions suggesting that transposable elements` activity and accumulation may counteract the decrease of genome-wide diversity following domestication. In addition, eco-geographical sub-genome pools of the cultivated barley were identified in support to the theory of multiple origins of domestication within the genus Hordeum. We also provide conclusions about the relationship between accessions of different species and the putative routes of barley domestication. In conclusion, the retrotransposon BARE-1 stands as a reliable and perspective DNA marker for the assessment of the phylogenetic and domestication history in the genus Hordeum and other crop species.

Molecular evidence of RNA polymerase II gene reveals the origin of worldwide cultivated barley

The origin and domestication of cultivated barley have long been under debate. A population-based resequencing and phylogenetic analysis of the single copy of RPB2 gene was used to address barley domestication, to explore genetic differentiation of barley populations on the worldwide scale, and to understand gene-pool exchanges during the spread and subsequent development of barley cultivation. Our results revealed significant genetic differentiation among three geographically distinct wild barley populations. Differences in haplotype composition among populations from different geographical regions revealed that modern cultivated barley originated from two major wild barley populations: one from the Near East Fertile Crescent and the other from the Tibetan Plateau, supporting polyphyletic origin of cultivated barley. The results of haplotype frequencies supported multiple domestications coupled with widespread introgression events that generated genetic admixture between divergent barley gene pools. Our results not only provide important insight into the domestication and evolution of cultivated barley, but also enhance our understanding of introgression and distinct selection pressures in different environments on shaping the genetic diversity of worldwide barley populations, thus further facilitating the effective use of the wild barley germplasm.

Population structure and marker-trait association of salt tolerance in barley (Hordeum vulgare L.)

Association mapping is becoming an important tool for identifying alleles and loci responsible for dissecting highly complex traits in barley. This study describes the population structure and marker-trait association using general linear model (GLM) analysis on a site of 60 barley genotypes, evaluated in six salinity environments. Ninety-eight SSR and SNP alleles were employed for the construction of a framework genetic map. The genetic structure analysis of the collection turned out to consist of two major sub-populations, mainly comprising hulled and naked types. LD significantly varied among the barley chromosomes, suggesting that this factor may affect the resolution of association mapping for QTL located on different chromosomes. Numerous significant marker traits were associated in different regions of the barley genome controlling salt tolerance and related traits; among them, 46 QTLs were detected on 14 associated traits over the two years, with a major QTL controlling salt tolerance on 1H, 2H, 4H and 7H, which are important factors in improving barley's salt tolerance.

The Role of Deleterious Substitutions in Crop Genomes

Populations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects of new mutations is not directly observable, many mutations likely either have no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r(2) = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm.

Germplasm dynamics: the role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne

Perennial ryegrass (Lolium perenne) is the most widely grown temperate grass species globally. Intensive plant breeding in ryegrass compared to many other crops species is a relatively recent exercise (last 100 years) and provides an interesting experimental system to trace the extent, impact and trajectory of undomesticated ecotypic variation represented in modern ryegrass cultivars. To explore germplasm dynamics in Lolium perenne, 2199 SNPs were genotyped in 716 ecotypes sampled from 90 European locations together with 249 cultivars representing 33 forage/amenity accessions. In addition three pseudo-cross mapping populations (450 individual recombinants) were genotyped to create a consensus genetic linkage map. Multivariate analyses revealed strong differentiation between cultivars with a small proportion of the ecotypic variation captured in improved cultivars. Ryegrass cultivars generated as part of a recurrent selection programme (RSP) are strongly associated with a small number of geographically localised Italian ecotypes which were among the founders of the RSP. Changes in haplotype frequency revealed signatures of selection in genes putatively involved in water-soluble carbohydrate (WSC) accumulation (a trait selected in the RSP). Retrospective analysis of germplasm in breeding programmes (germplasm dynamics) provides an experimental framework for the identification of candidate genes for novel traits such as WSC accumulation in ryegrass.

Association Analysis in Rice: From Application to Utilization

Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding.

Next generation breeding

The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders' needs to revolutionize crop improvement.

Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii

Using GWAS, 13 significant SNPs distributed on six of the seven Aegilops tauschii chromosomes (all but 5D) were identified, and several candidate P-deficiency-responsive genes were proposed from searches of public databases. Aegilops tauschii, the wheat (Triticum aestivum) D-genome progenitor, possesses numerous genes for stress resistance, including genes for tolerance of phosphorus (P) deficiency. Investigation of the genetic architecture of A. tauschii will help in developing P-deficiency-tolerant varieties of wheat. We evaluated nine traits in a population of 380 A. tauschii specimens under conditions with and without P application, and we performed genome-wide association studies for these traits using single nucleotide polymorphism (SNP) chips containing 7185 markers. Using a general linear model, we identified 119 SNPs that were significantly associated with all nine traits, and a mixed linear model revealed 18 SNPs associated with all traits. Both models detected 13 significant markers distributed on six of the seven A. tauschii chromosomes (all but 5D). Searches of public databases revealed several candidate/flanking genes related to P-deficiency tolerance. These genes were grouped in five categories by the types of proteins they encoded: defense response proteins, enzymes, promoters and transcription factors, storage proteins, or proteins triggered by P deficiency. The identified SNPs and genes contain essential information for cloning genes related to P-deficiency tolerance in A. tauschii and wheat, and they provide a foundation for breeding P-deficiency tolerant wheat cultivars.

Genetic Diversity and Population Structure of Collard Landraces and their Relationship to Other Brassica oleracea Crops

Landraces have the potential to provide a reservoir of genetic diversity for crop improvement to combat the genetic erosion of the food supply. A landrace collection of the vitamin-rich specialty crop collard (Brassica oleracea L. var. viridis) was genetically characterized to assess its potential for improving the diverse crop varieties of B. oleracea. We used the Illumina 60K Brassica SNP BeadChip array with 52,157 single nucleotide polymorphisms (SNPs) to (i) clarify the relationship of collard to the most economically important B. oleracea crop types, (ii) evaluate genetic diversity and population structure of 75 collard landraces, and (iii) assess the potential of the collection for genome-wide association studies (GWAS) through characterization of genomic patterns of linkage disequilibrium. Confirming the collection as a valuable genetic resource, the collard landraces had twice the polymorphic markers (11,322 SNPs) and 10 times the variety-specific alleles (521 alleles) of the remaining crop types examined in this study. On average, linkage disequilibrium decayed to background levels within 600 kilobase (kb), allowing for sufficient coverage of the genome for GWAS using the physical positions of the 8273 SNPs polymorphic among the landraces. Although other relationships varied, the previous placement of collard with the cabbage family was confirmed through phylogenetic analysis and principal coordinates analysis (PCoA).

A Scale-Corrected Comparison of Linkage Disequilibrium Levels between Genic and Non-Genic Regions

The understanding of non-random association between loci, termed linkage disequilibrium (LD), plays a central role in genomic research. Since causal mutations are generally not included in genomic marker data, LD between those and available markers is essential for capturing the effects of causal loci on localizing genes responsible for traits. Thus, the interpretation of association studies requires a detailed knowledge of LD patterns. It is well known that most LD measures depend on minor allele frequencies (MAF) of the considered loci and the magnitude of LD is influenced by the physical distances between loci. In the present study, a procedure to compare the LD structure between genomic regions comprising several markers each is suggested. The approach accounts for different scaling factors, namely the distribution of MAF, the distribution of pair-wise differences in MAF, and the physical extent of compared regions, reflected by the distribution of pair-wise physical distances. In the first step, genomic regions are matched based on similarity in these scaling factors. In the second step, chromosome- and genome-wide significance tests for differences in medians of LD measures in each pair are performed. The proposed framework was applied to test the hypothesis that the average LD is different in genic and non-genic regions. This was tested with a genome-wide approach with data sets for humans (Homo sapiens), a highly selected chicken line (Gallus gallus domesticus) and the model plant Arabidopsis thaliana. In all three data sets we found a significantly higher level of LD in genic regions compared to non-genic regions. About 31% more LD was detected genome-wide in genic compared to non-genic regions in Arabidopsis thaliana, followed by 13.6% in human and 6% chicken. Chromosome-wide comparison discovered significant differences on all 5 chromosomes in Arabidopsis thaliana and on one third of the human and of the chicken chromosomes.

Nucleotide diversity patterns of three divergent soybean populations: evidences for population-dependent linkage disequilibrium and taxonomic status of Glycine gracilis

The level of linkage disequilibrium (LD) is a major factor to determine DNA polymorphism pattern of a population and to construct high‐resolution maps useful in localizing and gene cloning of complicated traits. Here, we investigated LD level of three soybean populations with different genetic backgrounds and taxonomic status of G. gracilis by comparing the DNA polymorphism patterns of four high‐diversity single‐copy nuclear genes. A total of 152, 22, and 77 accessions of G. soja, G. gracilis, and G. max were observed. The results indicated that G. max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G. soja. Four gene loci evolved according to neutrality in both G. max and G. gracilis populations, and three gene loci evolved according to neutrality in G. soja population by Tajima's and Fu and Li's test. However, one gene locus deviated from neutrality by Fu and Li's test in the G. soja population. Further, medial level of LD (average r² = 0.2426) was found in intragene in G. max and G. gracilis populations, but unexpected low level of LD (r² ≤ 0.0539) was found in G. soja population. Significant genetic differentiation was detected between G. max and G. soja populations and also between G. max and G. gracilis populations; however, nonsignificant genetic differentiation was found between G. gracilis and G. soja populations. The results suggest that LD level depends on genetic background of soybean population, and implicit that G. gracilis should be regarded as the variant of G. soja, not as an independent species.

Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping

To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.

Barley: a translational model for adaptation to climate change

Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes - including examples that are indicative of the complexities involved in designing appropriate responses - are presented, and key developments for the future highlighted.

Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel

Rapid LD decay in wild emmer population from Israel allows high-resolution association mapping. Known and putative new stripe rust resistance genes were found. Genome-wide association mapping (GWAM) is becoming an important tool for the discovery and mapping of loci underlying trait variation in crops, but in the wild relatives of crops the use of GWAM has been limited. Critical factors for the use of GWAM are the levels of linkage disequilibrium (LD) and genetic diversity in mapped populations, particularly in those of self-pollinating species. Here, we report LD estimation in a population of 128 accessions of self-pollinating wild emmer, Triticum turgidum ssp. dicoccoides, the progenitor of cultivated wheat, collected in Israel. LD decayed fast along wild emmer chromosomes and reached the background level within 1 cM. We employed GWAM for the discovery and mapping of genes for resistance to three isolates of Puccinia striiformis, the causative agent of wheat stripe rust. The wild emmer population was genotyped with the wheat iSelect assay including 8643 gene-associated SNP markers (wheat 9K Infinium) of which 2,278 were polymorphic. The significance of association between stripe rust resistance and each of the polymorphic SNP was tested using mixed linear model implemented in EMMA software. The model produced satisfactory results and uncovered four significant associations on chromosome arms 1BS, 1BL and 3AL. The locus on 1BS was located in a region known to contain stripe rust resistance genes. These results show that GWAM is an effective strategy for gene discovery and mapping in wild emmer that will accelerate the utilization of this genetic resource in wheat breeding.

Evolutionary history of wild barley (Hordeum vulgare subsp. spontaneum) analyzed using multilocus sequence data and paleodistribution modeling

Studies of Hordeum vulgare subsp. spontaneum, the wild progenitor of cultivated barley, have mostly relied on materials collected decades ago and maintained since then ex situ in germplasm repositories. We analyzed spatial genetic variation in wild barley populations collected rather recently, exploring sequence variations at seven single-copy nuclear loci, and inferred the relationships among these populations and toward the genepool of the crop. The wild barley collection covers the whole natural distribution area from the Mediterranean to Middle Asia. In contrast to earlier studies, Bayesian assignment analyses revealed three population clusters, in the Levant, Turkey, and east of Turkey, respectively. Genetic diversity was exceptionally high in the Levant, while eastern populations were depleted of private alleles. Species distribution modeling based on climate parameters and extant occurrence points of the taxon inferred suitable habitat conditions during the ice-age, particularly in the Levant and Turkey. Together with the ecologically wide range of habitats, they might contribute to structured but long-term stable populations in this region and their high genetic diversity. For recently collected individuals, Bayesian assignment to geographic clusters was generally unambiguous, but materials from genebanks often showed accessions that were not placed according to their assumed geographic origin or showed traces of introgression from cultivated barley. We assign this to gene flow among accessions during ex situ maintenance. Evolutionary studies based on such materials might therefore result in wrong conclusions regarding the history of the species or the origin and mode of domestication of the crop, depending on the accessions included.