Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

Single Gene ◽

Genome Wide Association ◽

Chromosome 1 ◽

Whole Genome ◽

Sclerotinia Stem Rot ◽

Genome Wide ◽

A Genome ◽

Abstract Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm . A single gene (Glyma.01g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. These results suggest that this region harbors a promising resistance QTL to SSR that can be used in soybean breeding program.

Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

10.21203/rs.2.14709/v5 ◽

2020 ◽

Author(s):

Chiheb Boudhrioua ◽

Maxime Bastien ◽

Davoud Torkamaneh ◽

François Belzile

Keyword(s):

Association Mapping ◽

Single Gene ◽

Genome Wide Association ◽

Chromosome 1 ◽

Whole Genome ◽

Sclerotinia Stem Rot ◽

Genome Wide ◽

A Genome ◽

Abstract Background: Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. Results: In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm . A single gene (Glyma.01g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. Conclusion: These results suggest that the new region on chromosome 1 harbors a promising resistance QTL to SSR that can be used in soybean breeding program.

Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

10.21203/rs.2.14709/v3 ◽

2020 ◽

Author(s):

Chiheb Boudhrioua ◽

Maxime Bastien ◽

Davoud Torkamaneh ◽

François Belzile

Keyword(s):

Association Mapping ◽

Single Gene ◽

Genome Wide Association ◽

Chromosome 1 ◽

Whole Genome ◽

Sclerotinia Stem Rot ◽

Genome Wide ◽

A Genome ◽

Abstract Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm . A single gene (Glyma.01g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. These results suggest that this region harbors a promising resistance QTL to SSR that can be used in soybean breeding program.

Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

10.21203/rs.2.14709/v1 ◽

2019 ◽

Author(s):

Chiheb Boudhrioua ◽

Maxime Bastien ◽

Davoud Torkamaneh ◽

François Belzile

Keyword(s):

Association Mapping ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Chromosome 1 ◽

Whole Genome ◽

Sclerotinia Stem Rot ◽

Genome Wide ◽

A Genome ◽

Abstract Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Gm01) where resistant lines had shorter lesions on the stem by 29 mm. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Gm01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. These results suggest that this region harbors a promising resistance QTL to SSR that can be used in soybean breeding program.

Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

BMC Plant Biology ◽

10.1186/s12870-020-02401-8 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Chiheb Boudhrioua ◽

Maxime Bastien ◽

Davoud Torkamaneh ◽

François Belzile

Keyword(s):

Association Mapping ◽

Genome Wide Association ◽

Whole Genome ◽

Genome Resequencing ◽

Genome Wide ◽

Whole Genome Resequencing

Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Genes ◽

10.3390/genes12121897 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1897

Author(s):

Endale G. Tafesse ◽

Krishna K. Gali ◽

V. B. Reddy Lachagari ◽

Rosalind Bueckert ◽

Thomas D. Warkentin

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Vegetation Index ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Adaptive Traits ◽

Flowering Duration ◽

Genome Wide ◽

A Genome

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

Genome-wide association study reveals 14 new SNPs and confirms two structural variants highly associated with the horned/polled phenotype in goats

BMC Genomics ◽

10.1186/s12864-021-08089-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jiazhong Guo ◽

Rui Jiang ◽

Ayi Mao ◽

George E. Liu ◽

Siyuan Zhan ◽

...

Keyword(s):

Association Study ◽

Mixed Model ◽

Genome Wide Association Study ◽

Insertion Site ◽

Genome Wide Association ◽

Chromosome 1 ◽

Structural Variants ◽

Diagnostic Pcr ◽

Genome Wide ◽

A Genome

Abstract Background There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats. Results We obtained a total of 13,980,209 biallelic SNPs, using the genotyping-by-sequencing data from 45 Jintang Black (JT) goats, which included 32 female and nine male goats, and four individuals with the polled intersex syndrome (PIS). Using a mixed-model based GWAS, we identified two association signals, which were located at 150,334,857–150,817,260 bp (P = 5.15 × 10− 119) and 128,286,704–131,306,537 bp (P = 2.74 × 10− 15) on chromosome 1. The genotype distributions of the 14 most significantly associated SNPs were completely correlated with horn status in goats, based on the whole-genome sequencing (WGS) data from JT and two other Chinese horned breeds. However, variant annotation suggested that none of the detected SNPs within the associated regions were plausible causal mutations. Via additional read-depth analyses and visual inspections of WGS data, we found a 10.1-kb deletion (CHI1:g. 129424781_129434939del) and a 480-kb duplication (CHI1:150,334,286–150,818,098 bp) encompassing two genes KCNJ15 and ERG in the associated regions of polled and PIS-affected goats. Notably, the 10.1-kb deletion also served as the insertion site for the 480-kb duplication, as validated by PCR and Sanger sequencing. Our WGS genotyping showed that all horned goats were homozygous for the reference alleles without either the structural variants (SVs), whereas the PIS-affected goats were homozygous for both the SVs. We also demonstrated that horned, polled, and PIS-affected individuals among 333 goats from JT and three other Chinese horned breeds can be accurately classified via PCR amplification and agarose gel electrophoresis of two fragments in both SVs. Conclusion Our results revealed that two genomic regions on chromosome 1 are major loci affecting the polled phenotypes in goats. We provided a diagnostic PCR to accurately classify horned, polled, and PIS-affected goats, which will enable a reliable genetic test for the early-in-life prediction of horn status in goats.

Genome-wide association study and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness

Scientific Reports ◽

10.1038/s41598-019-50573-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Rueben G. Das ◽

Doreen Becker ◽

Vidhya Jagannathan ◽

Orly Goldstein ◽

Evelyn Santana ◽

...

Keyword(s):

Association Study ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Night Blindness ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Whole Genome ◽

Congenital Stationary Night Blindness ◽

Genome Wide ◽

A Genome

Abstract Congenital stationary night blindness (CSNB), in the complete form, is caused by dysfunctions in ON-bipolar cells (ON-BCs) which are secondary neurons of the retina. We describe the first disease causative variant associated with CSNB in the dog. A genome-wide association study using 12 cases and 11 controls from a research colony determined a 4.6 Mb locus on canine chromosome 32. Subsequent whole-genome sequencing identified a 1 bp deletion in LRIT3 segregating with CSNB. The canine mutant LRIT3 gives rise to a truncated protein with unaltered subcellular expression in vitro. Genetic variants in LRIT3 have been associated with CSNB in patients although there is limited evidence regarding its apparently critical function in the mGluR6 pathway in ON-BCs. We determine that in the canine CSNB retina, the mutant LRIT3 is correctly localized to the region correlating with the ON-BC dendritic tips, albeit with reduced immunolabelling. The LRIT3-CSNB canine model has direct translational potential enabling studies to help understand the CSNB pathogenesis as well as to develop new therapies targeting the secondary neurons of the retina.

Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping

Phytopathology ◽

10.1094/phyto-10-19-0372-r ◽

2020 ◽

Vol 110 (4) ◽

pp. 881-891 ◽

Cited By ~ 5

Author(s):

Anke Martin ◽

Paula Moolhuijzen ◽

Yongfu Tao ◽

Judy McIlroy ◽

Simon R. Ellwood ◽

...

Keyword(s):

Association Mapping ◽

Population Level ◽

Genome Wide Association ◽

Pyrenophora Teres ◽

Barley Cultivars ◽

Genome Wide ◽

A Genome ◽

Sexual Recombination ◽

Parastagonospora Nodorum ◽

Genomic Regions

Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.