Genome-wide association mapping of lentil (Lens culinaris Medikus) prebiotic carbohydrates toward improved human health and crop stress tolerance

AbstractLentil, a cool-season food legume, is rich in protein and micronutrients with a range of prebiotic carbohydrates, such as raffinose-family oligosaccharides (RFOs), fructooligosaccharides (FOSs), sugar alcohols (SAs), and resistant starch (RS), which contribute to lentil's health benefits. Beneficial microorganisms ferment prebiotic carbohydrates in the colon, which impart health benefits to the consumer. In addition, these carbohydrates are vital to lentil plant health associated with carbon transport, storage, and abiotic stress tolerance. Thus, lentil prebiotic carbohydrates are a potential nutritional breeding target for increasing crop resilience to climate change with increased global nutritional security. This study phenotyped a total of 143 accessions for prebiotic carbohydrates. A genome-wide association study (GWAS) was then performed to identify associated variants and neighboring candidate genes. All carbohydrates analyzed had broad-sense heritability estimates (H2) ranging from 0.22 to 0.44, comparable to those reported in the literature. Concentration ranges corresponded to percent recommended daily allowances of 2–9% SAs, 7–31% RFOs, 51–111% RS, and 57–116% total prebiotic carbohydrates. Significant SNPs and associated genes were identified for numerous traits, including a galactosyltransferase (Lcu.2RBY.1g019390) known to aid in RFO synthesis. Further studies in multiple field locations are necessary. Yet, these findings suggest the potential for molecular-assisted breeding for prebiotic carbohydrates in lentil to support human health and crop resilience to increase global food security.

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A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400987 ◽

2020 ◽

Vol 10 (5) ◽

pp. 1685-1696

Author(s):

Lorenzo Stagnati ◽

Vahid Rahjoo ◽

Luis F. Samayoa ◽

James B. Holland ◽

Virginia M. G. Borrelli ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Germination Rate ◽

Fusarium Verticillioides ◽

Screening Method ◽

Significant Snps ◽

Genome Wide Association ◽

Genome Wide ◽

Seedling Length ◽

A Genome

Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides.

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A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton

Genes ◽

10.3390/genes10100829 ◽

2019 ◽

Vol 10 (10) ◽

pp. 829 ◽

Cited By ~ 1

Author(s):

Muhammad Yasir ◽

Shoupu He ◽

Gaofei Sun ◽

Xiaoli Geng ◽

Zhaoe Pan ◽

...

Keyword(s):

Salt Tolerance ◽

Association Study ◽

Stress Tolerance ◽

Salinity Stress ◽

Upland Cotton ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Salinity Stress Tolerance

Millions of hectares of land are too saline to produce economically valuable crop yields. Salt tolerance in cotton is an imperative approach for improvement in response to ever-increasing soil salinization. Little is known about the genetic basis of salt tolerance in cotton at the seedling stage. To address this issue, a genome-wide association study (GWAS) was conducted on a core collection of a genetically diverse population of upland cotton (Gossypium hirsutum L.) comprising of 419 accessions, representing various geographic origins, including China, USA, Pakistan, the former Soviet Union, Chad, Australia, Brazil, Mexico, Sudan, and Uganda. Phenotypic evaluation of 7 traits under control (0 mM) and treatment (150 mM) NaCl conditions depicted the presence of broad natural variation in the studied population. The association study was carried out with the efficient mixed-model association eXpedited software package. A total of 17,264 single-nucleotide polymorphisms (SNPs) associated with different salinity stress tolerance related traits were found. Twenty-three candidate SNPs related to salinity stress-related traits were selected. Final key SNPs were selected based on the r2 value with nearby SNPs in a linkage disequilibrium (LD) block. Twenty putative candidate genes surrounding SNPs, A10_95330133 and D10_61258588, associated with leaf relative water content, RWC_150, and leaf fresh weight, FW_150, were identified, respectively. We further validated the expression patterns of twelve candidate genes with qRT-PCR, which revealed different expression levels in salt-tolerant and salt-sensitive genotypes. The results of our GWAS provide useful knowledge about the genetic control of salt tolerance at the seedling stage, which could assist in elucidating the genetic and molecular mechanisms of salinity stress tolerance in cotton plants.

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Exploring the Genetic Architecture of Root-Related Traits in Mediterranean Bread Wheat Landraces by Genome-Wide Association Analysis

Agronomy ◽

10.3390/agronomy10050613 ◽

2020 ◽

Vol 10 (5) ◽

pp. 613 ◽

Cited By ~ 1

Author(s):

Rubén Rufo ◽

Silvio Salvi ◽

Conxita Royo ◽

Jose Soriano

Keyword(s):

Molecular Markers ◽

Bread Wheat ◽

Root Development ◽

Genome Wide Association Study ◽

Abiotic Stress Tolerance ◽

Genome Wide Association ◽

Mediterranean Countries ◽

Genome Wide ◽

A Genome ◽

Wheat Landraces

Background: Roots are essential for drought adaptation because of their involvement in water and nutrient uptake. As the study of the root system architecture (RSA) is costly and time-consuming, it is not generally considered in breeding programs. Thus, the identification of molecular markers linked to RSA traits is of special interest to the breeding community. The reported correlation between the RSA of seedlings and adult plants simplifies its assessment. Methods: In this study, a panel of 170 bread wheat landraces from 24 Mediterranean countries was used to identify molecular markers associated with the seminal RSA and related traits: seminal root angle, total root number, root dry weight, seed weight and shoot length, and grain yield (GY). Results: A genome-wide association study identified 135 marker-trait associations explaining 6% to 15% of the phenotypic variances for root related traits and 112 for GY. Fifteen QTL hotspots were identified as the most important for controlling root trait variation and were shown to include 31 candidate genes related to RSA traits, seed size, root development, and abiotic stress tolerance (mainly drought). Co-location for root related traits and GY was found in 17 genome regions. In addition, only four out of the fifteen QTL hotspots were reported previously. Conclusions: The variability found in the Mediterranean wheat landraces is a valuable source of root traits to introgress into adapted phenotypes through marker-assisted breeding. The study reveals new loci affecting root development in wheat.

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A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

10.1101/418509 ◽

2018 ◽

Cited By ~ 1

Author(s):

Veena Devi Ganeshan ◽

Stephen O. Opiyo ◽

Samuel K. Mutiga ◽

Felix Rotich ◽

David M. Thuranira ◽

...

Keyword(s):

Association Study ◽

Magnaporthe Oryzae ◽

Genome Wide Association Study ◽

Significant Snps ◽

Sub Saharan Africa ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Sub Saharan ◽

Genomic Regions

ABSTRACTThe fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.

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A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.)

Genes ◽

10.3390/genes11070759 ◽

2020 ◽

Vol 11 (7) ◽

pp. 759 ◽

Cited By ~ 1

Author(s):

Caleb Manamik Breria ◽

Ching-Hsiang Hsieh ◽

Tsair-Bor Yen ◽

Jo-Yi Yen ◽

Thomas J. Noble ◽

...

Keyword(s):

Salt Stress ◽

Association Study ◽

Stress Tolerance ◽

Vigna Radiata ◽

Genome Wide Association Study ◽

Chromosome 9 ◽

Genome Wide Association ◽

Salt Stress Tolerance ◽

Genome Wide ◽

A Genome

Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene Vradi07g01630, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes Vradi09g09510 and Vradi09g09600, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.

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A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries)

Scientific Reports ◽

10.1038/srep21111 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 7

Author(s):

Xue Ren ◽

Guang-Li Yang ◽

Wei-Feng Peng ◽

Yong-Xin Zhao ◽

Min Zhang ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Close Association ◽

Significant Snps ◽

Genomic Region ◽

Ovis Aries ◽

Genome Wide Association ◽

Chromosome 2 ◽

Genome Wide ◽

A Genome

Abstract Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.

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Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Heredity ◽

10.1038/s41437-020-00365-x ◽

2020 ◽

Author(s):

Yanhua Zhang ◽

Yuzhe Wang ◽

Yiyi Li ◽

Junfeng Wu ◽

Xinlei Wang ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Growth Traits ◽

Carcass Traits ◽

Significant Snps ◽

Genome Wide Association ◽

Pathway Enrichment Analysis ◽

Genome Wide ◽

A Genome ◽

Genetic Mechanisms

Abstract Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

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Genome-wide association mapping for agronomic and quality traits in foxtail millet

10.21203/rs.2.10042/v1 ◽

2019 ◽

Author(s):

Yanhong Lou ◽

Yun Chen ◽

Zhihao Liu ◽

Mingjie Sun ◽

Fei Han ◽

...

Keyword(s):

Genome Wide Association Study ◽

Foxtail Millet ◽

Significant Snps ◽

Genomic Variation ◽

Genome Wide Association ◽

Quality Traits ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Genome Wide ◽

A Genome

Abstract Background: Foxtail millet [Setaria italica (L.) P. Beauv.] is a particularly important cereal and fodder crop in arid and semi-arid regions. The genomic variation and alleles underpinning agronomic and quality traits are important for foxtail millet improvement. To better understand the diversity of foxtail millet and facilitate the genetic dissection of its agronomic and quality traits, we used high-quality single nucleotide polymorphisms (SNPs) to perform a genome-wide association study (GWAS). Results: Using genotyping-by-sequencing, 107 foxtail millet accessions were sequenced, and further analysis revealed 72,181 high-quality SNPs, of which 53 were significantly associated with 15 agronomic and quality traits. These SNPs were distributed across the nine chromosomes of foxtail millet; 44 were located in intergenic regions, whereas one and eight SNPs were located in exon and intron regions, respectively. The GWAS revealed that 28 SNPs were associated with a single trait. Conclusions: For some of the significant SNPs, favourable genotypes showed pyramiding effects for several traits. The 53 loci identified in this study will therefore be useful for breeding programs aimed at foxtail millet improvement.

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Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study

BMC Plant Biology ◽

10.1186/s12870-021-03299-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhengfu Zhou ◽

Huiyue Guan ◽

Congcong Liu ◽

Ziwei Zhang ◽

Shenghui Geng ◽

...

Keyword(s):

Association Study ◽

Candidate Gene ◽

Genome Wide Association Study ◽

Significant Snps ◽

Regulatory Elements ◽

Genome Wide Association ◽

Genetic Loci ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Abstract Background Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat. Results Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59–12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000. Conclusions To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat.

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Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed

Animals ◽

10.3390/ani11061531 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1531

Author(s):

Yasemin Öner ◽

Malena Serrano ◽

Pilar Sarto ◽

Laura Pilar Iguácel ◽

María Piquer-Sabanza ◽

...

Keyword(s):

Somatic Cell ◽

Genome Wide Association Study ◽

Association Studies ◽

Significant Snps ◽

Genome Wide Association ◽

System Response ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

A Genome

A genome-wide association study (GWAS) was performed to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium® HD SNP BeadChip (680K). In total, 6173 records from 1894 multiparous Assaf ewes with at least three test day records and aged between 2 and 7 years old were used to estimate a corrected phenotype for somatic cell score (SCS). Then, 192 ewes were selected from the top (n = 96) and bottom (n = 96) tails of the corrected SCS phenotype distribution to be used in a GWAS. Although no significant SNPs were found at the genome level, four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424) were significant at the chromosome level (FDR 10%) in two different regions of OAR19. The SNP rs419096188 was located in intron 1 of the NUP210 and close to the HDAC11 genes (61 kb apart), while the other three SNPs were totally linked and located 171 kb apart from the ARPP21 gene. These three genes were related to the immune system response. These results were validated in two SNPs (rs419096188 and rs424642424) in the total population (n = 1894) by Kompetitive Allele-Specific PCR (KASP) genotyping. Furthermore, rs419096188 was also associated with lactose content.

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