scholarly journals Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mahesh Pujar ◽  
S. Gangaprasad ◽  
Mahalingam Govindaraj ◽  
Sunil S. Gangurde ◽  
A. Kanatti ◽  
...  
Keyword(s):  
Association Study ◽  
Protein Content ◽  
Pearl Millet ◽  
Genome Wide Association Study ◽  
Breeding Strategy ◽  
Genome Wide Association ◽  
Late Embryogenesis Abundant Protein ◽  
Pentatricopeptide Repeat ◽  
Genome Wide ◽  
Population Structure Analysis

Abstract Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.

scholarly journals Genome-wide association study identified candidate genes for seed size and seed composition improvement in M. truncatula

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhijuan Chen ◽  
Vanessa Lancon-Verdier ◽  
Christine Le Signor ◽  
Yi-Min She ◽  
Yun Kang ◽  
...  
Keyword(s):  
Association Study ◽  
Protein Content ◽  
Seed Size ◽  
Seed Protein ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Strong Positive Correlation ◽  
Seed Composition ◽  
Seed Traits ◽  
Genome Wide

AbstractGrain legumes are highly valuable plant species, as they produce seeds with high protein content. Increasing seed protein production and improving seed nutritional quality represent an agronomical challenge in order to promote plant protein consumption of a growing population. In this study, we used the genetic diversity, naturally present in Medicago truncatula, a model plant for legumes, to identify genes/loci regulating seed traits. Indeed, using sequencing data of 162 accessions from the Medicago HAPMAP collection, we performed genome-wide association study for 32 seed traits related to seed size and seed composition such as seed protein content/concentration, sulfur content/concentration. Using different GWAS and postGWAS methods, we identified 79 quantitative trait nucleotides (QTNs) as regulating seed size, 41 QTNs for seed composition related to nitrogen (i.e. storage protein) and sulfur (i.e. sulfur-containing amino acid) concentrations/contents. Furthermore, a strong positive correlation between seed size and protein content was revealed within the selected Medicago HAPMAP collection. In addition, several QTNs showed highly significant associations in different seed phenotypes for further functional validation studies, including one near an RNA-Binding Domain protein, which represents a valuable candidate as central regulator determining both seed size and composition. Finally, our findings in M. truncatula represent valuable resources to be exploitable in many legume crop species such as pea, common bean, and soybean due to its high synteny, which enable rapid transfer of these results into breeding programs and eventually help the improvement of legume grain production.

scholarly journals Genome-wide association study of rice rooting ability at the seedling stage

2020 ◽  
Author(s):  
Xin Xu ◽  
Junhua Ye ◽  
Yingying Yang ◽  
Mengchen Zhang ◽  
Qun Xu ◽  
...  
Keyword(s):  
Association Study ◽  
Root Length ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Root Number ◽  
Expression Levels ◽  
Rooting Ability ◽  
Genome Wide ◽  
Population Structure Analysis

Abstract BackgroundRice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.ResultsTo characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.ConclusionsThrough evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.

scholarly journals Mapping loci controlling fatty acid profiles, oil and protein content by genome-wide association study in Brassica napus

2019 ◽  
Vol 7 (2) ◽  
pp. 217-226 ◽  
Author(s):  
Minqiang Tang ◽  
Yuanyuan Zhang ◽  
Yueying Liu ◽  
Chaobo Tong ◽  
Xiaohui Cheng ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Brassica Napus ◽  
Association Study ◽  
Protein Content ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Fatty Acid Profiles ◽  
Genome Wide

Candidate genes and genome-wide association study of grain protein content and protein deviation in durum wheat

Planta ◽  
2019 ◽  
Vol 249 (4) ◽  
pp. 1157-1175 ◽  
Author(s):  
D. Nigro ◽  
A. Gadaleta ◽  
G. Mangini ◽  
P. Colasuonno ◽  
I. Marcotuli ◽  
...  
Keyword(s):  
Association Study ◽  
Durum Wheat ◽  
Protein Content ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Grain Protein Content ◽  
Genome Wide Association ◽  
Grain Protein ◽  
Genome Wide

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 Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage

2020 ◽  
Author(s):  
Xin Xu ◽  
Junhua Ye ◽  
Yingying Yang ◽  
Mengchen Zhang ◽  
Qun Xu ◽  
...  
Keyword(s):  
Association Study ◽  
Root Length ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Root Number ◽  
Expression Levels ◽  
Rooting Ability ◽  
Genome Wide ◽  
Population Structure Analysis

Abstract Background Rice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.Results To characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Combined with the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 32 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasms with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.Conclusions The goal of our research was to improve understanding of the genetic basis of rice rooting ability and provide useful molecular markers and germplasms for rice root breeding.

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