scholarly journals Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study

PLoS ONE ◽  
2019 ◽  
Vol 14 (10) ◽  
pp. e0224074 ◽  
Author(s):  
Namhee Jeong ◽  
Ki-Seung Kim ◽  
Seongmun Jeong ◽  
Jae-Yoon Kim ◽  
Soo-Kwon Park ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Study ◽  
Core Collection ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-wide association study in New York Phytophthora capsici isolates reveals loci involved in mating type and mefenoxam sensitivity

2020 ◽  
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

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.

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

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.

scholarly journals Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean (Phaseolus vulgaris) Core Collection

2021 ◽  
Vol 12 ◽  
Author(s):  
Ainong Shi ◽  
Paul Gepts ◽  
Qijian Song ◽  
Haizheng Xiong ◽  
Thomas E. Michaels ◽  
...  
Keyword(s):  
Association Study ◽  
Common Bean ◽  
Soybean Cyst Nematode ◽  
Core Collection ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Cyst Nematode ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Scn Resistance

Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.

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

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.

scholarly journals Genome-Wide Association Study in Wheat Identifies Resistance to the Cereal Cyst Nematode Heterodera filipjevi

2016 ◽  
Vol 106 (10) ◽  
pp. 1128-1138 ◽  
Author(s):  
Shree R. Pariyar ◽  
Abdelfattah A. Dababat ◽  
Wiebke Sannemann ◽  
Gul Erginbas-Orakci ◽  
Abdelnaser Elashry ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Cyst Nematode ◽  
Genome Wide Association ◽  
Cyst Nematodes ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome ◽  
Heterodera Filipjevi

The cyst nematode Heterodera filipjevi is a plant parasite causing substantial yield loss in wheat. Resistant cultivars are the preferred method of controlling cyst nematodes. Association mapping is a powerful approach to detect associations between phenotypic variation and genetic polymorphisms; in this way favorable traits such as resistance to pathogens can be located. Therefore, a genome-wide association study of 161 winter wheat accessions was performed with a 90K iSelect single nucleotide polymorphism (SNP) chip. Population structure analysis grouped into two major subgroups and first principal component accounted 6.16% for phenotypic diversity. The genome-wide linkage disequilibrium across wheat was 3 cM. Eleven quantitative trait loci (QTLs) on chromosomes 1AL, 2AS, 2BL, 3AL, 3BL, 4AS, 4AL, 5BL, and 7BL were identified using a mixed linear model false discovery rate of P < 0.01 that explained 43% of total genetic variation. This is the first report of QTLs conferring resistance to H. filipjevi in wheat. Eight QTLs on chromosomes 1AL, 2AS, 2BL, 3AL, 4AL, and 5BL were linked to putative genes known to be involved in plant−pathogen interactions. Two other QTLs on 3BL and one QTL on 7BL linked to putative genes known to be involved in abiotic stress.

scholarly journals Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Peng Zhang ◽  
Kaizhen Zhong ◽  
Zhengzheng Zhong ◽  
Hanhua Tong
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Core Collection ◽  
Genome Wide Association Study ◽  
High Rate ◽  
Genome Wide Association ◽  
Genetic Mechanism ◽  
Al Tolerance ◽  
Genome Wide ◽  
Significant Difference

Abstract Background The genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice. Results Genome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting’s core collection constructed from 2262 Ting’s collections with more than 3.8 million SNPs. Within Ting’s core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes like NRAT1, ART1 and STAR1 were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance. Conclusions The present study provided important information for further using these elite genes existing in Ting’s core collection for improvement of rice Al tolerance.

scholarly journals Genome wide association study of agronomic and seed traits in a world collection of proso millet (Panicum miliaceum L.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sameh Boukail ◽  
Mercy Macharia ◽  
Mara Miculan ◽  
Alberto Masoni ◽  
Alessandro Calamai ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Genome Wide Association ◽  
Seed Traits ◽  
Proso Millet ◽  
Genome Wide ◽  
World Collection ◽  
A Genome ◽  
Western Asia

Abstract Background The climate crisis threatens sustainability of crop production worldwide. Crop diversification may enhance food security while reducing the negative impacts of climate change. Proso millet (Panicum milaceum L.) is a minor cereal crop which holds potential for diversification and adaptation to different environmental conditions. In this study, we assembled a world collection of proso millet consisting of 88 varieties and landraces to investigate its genomic and phenotypic diversity for seed traits, and to identify marker-trait associations (MTA). Results Sequencing of restriction-site associated DNA fragments yielded 494 million reads and 2,412 high quality single nucleotide polymorphisms (SNPs). SNPs were used to study the diversity in the collection and perform a genome wide association study (GWAS). A genotypic diversity analysis separated accessions originating in Western Europe, Eastern Asia and Americas from accessions sampled in Southern Asia, Western Asia, and Africa. A Bayesian structure analysis reported four cryptic genetic groups, showing that landraces accessions had a significant level of admixture and that most of the improved proso millet materials clustered separately from landraces. The collection was highly diverse for seed traits, with color varying from white to dark brown and width spanning from 1.8 to 2.6 mm. A GWAS study for seed morphology traits identified 10 MTAs. In addition, we identified three MTAs for agronomic traits that were previously measured on the collection. Conclusion Using genomics and automated seed phenotyping, we elucidated phylogenetic relationships and seed diversity in a global millet collection. Overall, we identified 13 MTAs for key agronomic and seed traits indicating the presence of alleles with potential for application in proso breeding programs.

Sign in / Sign up

Export Citation Format

Share Document