North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

AbstractPhytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) State and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single-nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam insensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam insensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA Polymerase I, the enzyme that has been hypothesized to be the target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.

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Population structure and genetic basis of the stripe rust resistance of 140 Chinese wheat landraces revealed by a genome-wide association study

Plant Science ◽

10.1016/j.plantsci.2020.110688 ◽

2020 ◽

Vol 301 ◽

pp. 110688

Author(s):

Fangjie Yao ◽

Li Long ◽

Yuqi Wang ◽

Luyao Duan ◽

Xuyang Zhao ◽

...

Keyword(s):

Population Structure ◽

Association Study ◽

Rust Resistance ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Stripe Rust Resistance ◽

Genome Wide ◽

A Genome ◽

Chinese Wheat

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Genome-Wide Association Study in New York Phytophthora capsici Isolates Reveals Loci Involved in Mating Type and Mefenoxam Sensitivity

Phytopathology ◽

10.1094/phyto-04-20-0112-fi ◽

2020 ◽

pp. PHYTO-04-20-011

Author(s):

Gregory Vogel ◽

Michael A. Gore ◽

Christine D. Smart

Keyword(s):

New York ◽

Population Structure ◽

Association Study ◽

Candidate Genes ◽

Mating Type ◽

Genome Wide Association Study ◽

Phytophthora Capsici ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

Phytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) state and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam sensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam sensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA polymerase I, the hypothesized target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.

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Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions

Frontiers in Plant Science ◽

10.3389/fpls.2021.711654 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ana Borrego-Benjumea ◽

Adam Carter ◽

Min Zhu ◽

James R. Tucker ◽

Meixue Zhou ◽

...

Keyword(s):

Population Structure ◽

Association Study ◽

Phenotypic Variation ◽

Abiotic Stresses ◽

Genome Wide Association Study ◽

Field Conditions ◽

Genome Wide Association ◽

Waterlogging Tolerance ◽

Barley Breeding ◽

Genome Wide

Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8–11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.

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Genome-Wide Association Study of Anthracnose Resistance in Andean Beans (Phaseolus vulgaris)

PLoS ONE ◽

10.1371/journal.pone.0156391 ◽

2016 ◽

Vol 11 (6) ◽

pp. e0156391 ◽

Cited By ~ 47

Author(s):

Grady H. Zuiderveen ◽

Bilal A. Padder ◽

Kelvin Kamfwa ◽

Qijian Song ◽

James D. Kelly

Keyword(s):

Phaseolus Vulgaris ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Anthracnose Resistance ◽

Genome Wide

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Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs

Plant Biotechnology Journal ◽

10.1111/pbi.12722 ◽

2017 ◽

Vol 15 (11) ◽

pp. 1374-1386 ◽

Cited By ~ 65

Author(s):

Cong Huang ◽

Xinhui Nie ◽

Chao Shen ◽

Chunyuan You ◽

Wu Li ◽

...

Keyword(s):

Population Structure ◽

Association Study ◽

Upland Cotton ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

High Density ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

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Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance

Theoretical and Applied Genetics ◽

10.1007/s00122-021-04014-7 ◽

2022 ◽

Author(s):

Joris A. Alkemade ◽

Nelson Nazzicari ◽

Monika M. Messmer ◽

Paolo Annicchiarico ◽

Barbara Ferrari ◽

...

Keyword(s):

Association Study ◽

Candidate Gene ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

White Lupin ◽

Grain Legume ◽

Anthracnose Resistance ◽

Anthracnose Disease ◽

Genome Wide ◽

A Genome

Abstract Key message GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. Abstract White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.

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Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

10.21203/rs.2.20026/v1 ◽

2020 ◽

Author(s):

Waltram Ravelombola ◽

Jun Qin ◽

Ainong Shi ◽

Fengmin Wang ◽

Yan Feng ◽

...

Keyword(s):

Population Structure ◽

Association Study ◽

Genomic Selection ◽

Plant Height ◽

Seed Weight ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Snp Markers ◽

Genome Wide Association ◽

Genome Wide

Abstract BackgroundSoybean [Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy.Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). Population structure was inferred using STRUCTURE 2.3.4, GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that: a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci (E2, E4, and Dt1) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900, Glyma.19g200800, Glyma.09g196700, and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP (if no annotated genes found close the top one) for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent.Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits in soybean through marker-assisted selection (MAS) and GS in breeding programs. After validation, the candidate genes can be transferred to new cultivars using the linked SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

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Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight

PLoS ONE ◽

10.1371/journal.pone.0242500 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242500

Author(s):

Saher Islam ◽

Umesh K. Reddy ◽

Purushothaman Natarajan ◽

Venkata Lakshmi Abburi ◽

Amna Arshad Bajwa ◽

...

Keyword(s):

Body Weight ◽

Population Structure ◽

Association Study ◽

Milk Yield ◽

Genome Wide Association Study ◽

Water Buffalo ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Genome Wide ◽

Genomic Regions

The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.

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