scholarly journals Association Mapping for Drought Tolerance and Yield-Related Traits in Cowpea Accessions

2020 ◽  
Author(s):  
Gabriel Vusanimuzi Nkomo ◽  
Moosa Sedibe ◽  
Maletsema Alina Mofokeng ◽  
Rian Pierneef
Keyword(s):  
Drought Tolerance ◽  
Association Mapping ◽  
Linear Model ◽  
Genotyping By Sequencing ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Single Marker ◽  
Peak Of Delta

The objective of this study were to conduct association mapping for drought tolerance at the seedling stage and yield-related traits. 60 cowpea accessions were used in the study. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Association mapping was conducted using single-marker regression (SMR) in Q Gene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. The population of the cowpea accessions were analysed using STRUCTURE 2.3.4 and the peak of delta K in the greenhouse showed seven population types, whereas the peak of delta K in the glasshouse indicated the presence of six population types. One SNP marker, 14083649|F|0-9 was associated with NP with a p value <0.001. Fifty SNP markers were associated with PWT at p <0.001. Four SNP markers, 14074781|F|0-16, 100047392|F|0-36, 14083801|F|0-28 and 100051488|F|0-49 were associated with AVSPD at p <0.001. SNP markers, 14074781|F|0-16, 14083801|F|0-28 and 100051488|F|0-49 were associated with PL at P <0.001. Five SNP markers, 100047392|F|0-36, 14083801|F|0-28, 100072738|F|0-34, 14076881|F|0-49 and 14076881|F|0-49 were associated with PWDTH at p <0.001. The 65 SNP markers identified can be used in cowpea molecular breeding to select for AVSPD, NP, PL, PWDTH, PWT, and RR through marker assisted selection (MAS).

scholarly journals Population Structure and Association Analysis of Bolting, Plant Height, and Leaf Erectness in Spinach

HortScience ◽  
2016 ◽  
Vol 51 (5) ◽  
pp. 481-486 ◽  
Author(s):  
Jessica Chitwood ◽  
Ainong Shi ◽  
Beiquan Mou ◽  
Michael Evans ◽  
John Clark ◽  
...  
Keyword(s):  
Linear Model ◽  
Plant Height ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Structured Populations ◽  
United States Department ◽  
Nucleotide Polymorphisms ◽  
Single Marker

Spinach (Spinacia oleracea L.) is an important vegetable worldwide with high nutritional and health-promoting compounds. Bolting is an important trait to consider to grow spinach in different seasons and regions. Plant height and leaf erectness are important traits for machine harvesting. Breeding slow bolting, taller, and more erect spinach cultivars is needed for improved spinach production. A total of 288 United States Department of Agriculture (USDA) spinach accessions were used as the association panel in this research. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Two structured populations and the admixtures were inferred for the 288 spinach accession panel using STRUCTURE and MEGA. Association mapping was conducted using single-marker regression (SMR) in QGene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. Three SNP markers, AYZV02001321_398, AYZV02041012_1060, and AYZV02118171_95 were identified to be associated with bolting. Eight SNP markers, AYZV02014270_540, AYZV02250508_2162, AYZV02091523_19842, AYZV02141794_376, AYZV02077023_64, AYZV02210662_2532, AYZV02153224_2197, and AYZV02003975_248 were found to be associated with plant height. Four SNP markers, AYZV02188832_229, AYZV02219088_79, AYZV02030116_256, and AYZV02129827_197 were associated with erectness. These SNP markers may provide breeders with a tool in spinach molecular breeding to select spinach bolting, plant height, and erectness through marker-assisted selection (MAS).

scholarly journals Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1042
Author(s):  
Zhuoying Weng ◽  
Yang Yang ◽  
Xi Wang ◽  
Lina Wu ◽  
Sijie Hua ◽  
...  
Keyword(s):  
Fishery Management ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Individual Identification ◽  
Pedigree Information ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Polymorphic Snps ◽  
Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

Potential SNPs related to microspore culture in Raphanus sativus based on a single-marker analysis

2018 ◽  
Vol 98 (5) ◽  
pp. 1072-1083 ◽  
Author(s):  
Yong Suk Chung ◽  
Yun Gyeong Lee ◽  
Renato Rodrigues Silva ◽  
Suhyoung Park ◽  
Min Young Park ◽  
...  
Keyword(s):  
Raphanus Sativus ◽  
Microspore Culture ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Single Marker Analysis ◽  
Regeneration Rate ◽  
Marker Analysis ◽  
Wide Range ◽  
Single Marker ◽  
High Regeneration

Radish (Raphanus sativus) is an economically important crop grown for its edible roots and leaves. It is a self-incompatible, outcrossing species, making the production of homozygous lines and the development of breeding populations difficult. However, this can be overcome with haploids production techniques using isolated microspores, providing the rapid production of homozygous lines for breeding. Thus, it would be useful to identify radishes with a high regeneration rate from microspore culture. In the current study, 96 radish cultivars or germplasms were evaluated for high regeneration rates. Also, a single-marker analysis (SMA) was applied to detect single nucleotide polymorphisms (SNPs) potentially associated with this trait using genotype-by-sequencing (GBS) technology. The regeneration rate from microspore culture of 96 lines showed a wide range, from 0% to 269.5%. From the SMA, 52 markers were detected at a p value of 0.001 and a total of 11 physically nearby genes with high levels of similarity in various species were identified as candidates for high regeneration rates. This result could be used for clarifying the genetic basis underlying these traits and developing molecular markers associated with regeneration rates and would be beneficial for generating homozygous inbred lines.

scholarly journals Identification and Confirmation of Loci Associated With Canopy Wilting in Soybean Using Genome-Wide Association Mapping

2021 ◽  
Vol 12 ◽  
Author(s):  
Siva K. Chamarthi ◽  
Avjinder S. Kaler ◽  
Hussein Abdel-Haleem ◽  
Felix B. Fritschi ◽  
Jason D. Gillman ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Association Mapping ◽  
Candidate Genes ◽  
Stress Responses ◽  
Water Conservation ◽  
Production Systems ◽  
Block Design ◽  
Plant Stress ◽  
Significant Snps ◽  
Nucleotide Polymorphisms

Drought causes significant soybean [Glycine max (L.) Merr.] yield losses each year in rain-fed production systems of many regions. Genetic improvement of soybean for drought tolerance is a cost-effective approach to stabilize yield under rain-fed management. The objectives of this study were to confirm previously reported soybean loci and to identify novel loci associated with canopy wilting (CW) using a panel of 200 diverse maturity group (MG) IV accessions. These 200 accessions along with six checks were planted at six site-years using an augmented incomplete block design with three replications under irrigated and rain-fed treatments. Association mapping, using 34,680 single nucleotide polymorphisms (SNPs), identified 188 significant SNPs associated with CW that likely tagged 152 loci. This includes 87 SNPs coincident with previous studies that likely tagged 68 loci and 101 novel SNPs that likely tagged 84 loci. We also determined the ability of genomic estimated breeding values (GEBVs) from previous research studies to predict CW in different genotypes and environments. A positive relationship (P ≤ 0.05;0.37 ≤ r ≤ 0.5) was found between observed CW and GEBVs. In the vicinity of 188 significant SNPs, 183 candidate genes were identified for both coincident SNPs and novel SNPs. Among these 183 candidate genes, 57 SNPs were present within genes coding for proteins with biological functions involved in plant stress responses. These genes may be directly or indirectly associated with transpiration or water conservation. The confirmed genomic regions may be an important resource for pyramiding favorable alleles and, as candidates for genomic selection, enhancing soybean drought tolerance.

scholarly journals Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations

2017 ◽  
Vol 53 (No. 4) ◽  
pp. 159-167 ◽  
Author(s):  
K. Sethi ◽  
P. Siwach ◽  
S.K. Verma
Keyword(s):  
Linkage Disequilibrium ◽  
Association Mapping ◽  
Linear Model ◽  
Ssr Markers ◽  
Mixed Linear Model ◽  
Quality Traits ◽  
Fibre Quality ◽  
Gossypium Arboreum ◽  
Mixed Ancestry ◽  
Ssr Loci

Cotton productivity has been hindered by the narrow genetic base of cultivated cotton. Linkage disequilibrium-based association mapping has become a powerful molecular tool to dissect and exploit genetic diversity. In the present study, population structure and marker-trait associations for fibre quality traits in genotypes belonging to six races of Gossypium arboreum were assessed. Out of 300 simple sequence repeat (SSR) markers, 100 were found polymorphic, yielding a total of 240 alleles (all polymorphic). Structure analysis revealed allelic admixtures between genotypes. A Q-matrix exhibited mixed ancestry for the majority of genotypes, the race indicum forming a significant percent ancestry for almost all genotypes. At significant threshold values of r<sup>2</sup> ≥ 0.05, 7.37% of SSR loci showed significant linkage disequilibrium (LD), while at highly significant threshold of r<sup>2</sup> ≥ 0.1, the value was reduced to 5.31%. LD clearly decayed within the genetic distance of 9–10 cM, with r<sup>2</sup> ≥ 0.1. Twenty-eight SSR markers were found associated with six fibre quality traits using general linear model and mixed linear model.

scholarly journals Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans

Genes ◽  
2018 ◽  
Vol 10 (1) ◽  
pp. 5 ◽  
Author(s):  
Augusto Lima Diniz ◽  
Willian Giordani ◽  
Zirlane Portugal Costa ◽  
Gabriel R. A. Margarido ◽  
Juliana Morini K. C. Perseguini ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Association Mapping ◽  
Genotyping By Sequencing ◽  
Grain Legume ◽  
Human Consumption ◽  
Common Beans ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
True Association

Phaseolus vulgaris is an important grain legume for human consumption. Recently, association mapping studies have been performed for the species aiming to identify loci underlying quantitative variation of traits. It is now imperative to know whether the linkage disequilibrium (LD) reflects the true association between a marker and causative loci. The aim of this study was to estimate and analyze LD on a diversity panel of common beans using ordinary r2 and r2 extensions which correct bias due to population structure (rS2), kinship (rV2), and both (rVS2). A total of 10,362 single nucleotide polymorphisms (SNPs) were identified by genotyping by sequencing (GBS), and polymorphisms were found to be widely distributed along the 11 chromosomes. In terms of r2, high values of LD (over 0.8) were identified between SNPs located at opposite chromosomal ends. Estimates for rV2 were lower than those for rS2. Results for rV2 and rVS2 were similar, suggesting that kinship may also include information on population structure. Over genetic distance, LD decayed to 0.1 at a distance of 1 Mb for rVS2. Inter-chromosomal LD was also evidenced. This study showed that LD estimates decay dramatically according to the population structure, and especially the degree of kinship. Importantly, the LD estimates reported herein may influence our ability to perform association mapping studies on P. vulgaris.

scholarly journals Mixed Linear Model Approaches of Association Mapping for Complex Traits Based on Omics Variants

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Fu-Tao Zhang ◽  
Zhi-Hong Zhu ◽  
Xiao-Ran Tong ◽  
Zhi-Xiang Zhu ◽  
Ting Qi ◽  
...  
Keyword(s):  
Association Mapping ◽  
Linear Model ◽  
Complex Traits ◽  
Mixed Linear Model

scholarly journals Population genetic structure and association mapping for iron toxicity tolerance in rice

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0246232
Author(s):  
S. Pawar ◽  
E. Pandit ◽  
I. C. Mohanty ◽  
D. Saha ◽  
S. K. Pradhan
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Association Mapping ◽  
Stress Tolerance ◽  
Linear Model ◽  
Generalized Linear Model ◽  
Mixed Linear Model ◽  
Iron Toxicity ◽  
Rice Grain ◽  
Fe Toxicity

Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.

scholarly journals Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives

2020 ◽  
Author(s):  
Krishnanand P. Kulkarni ◽  
Nicholi Vorsa ◽  
Purushothaman Natarajan ◽  
Sathya Elavarthi ◽  
Massimo Iorizzo ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Vaccinium Corymbosum ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Admixture Analysis ◽  
Cross Derivatives ◽  
Southern Highbush

Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we used admixture and genetic relatedness analysis of northern highbush (NHB, V. corymbosum) and southern highbush (SHB, V. darrowii) blueberry genotypes and F2 progenies of the V. corymbosum &times; V. darrowii cross. Using genotyping-by-sequencing (GBS), we generated ~3.34 billion reads (75 bp). The GBS reads were aligned to the Vaccinium corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single nucleotide polymorphisms (SNPs), which were used for principal component, haplotype, and admixture analysis. PCA formed three main groups: 1) NHB cultivars, 2) SHB cultivars, and 3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB, indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mix of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived SNP markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.

scholarly journals Identification of drought-tolerance genes in the germination stage of soybean

2020 ◽  
Author(s):  
Xingzhen Zhao ◽  
Zhangxiong Liu ◽  
Huihui Li ◽  
Yanjun Zhang ◽  
Lili Yu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Seed Germination ◽  
Drought Tolerance ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Soybean Plants ◽  
Drought Tolerance Indices ◽  
Stress Influences ◽  
Tolerance Indices ◽  
Germination Stage

Abstract Background Drought stress influences the vigor of plant seeds and inhibits seed germination, making it one of the primary environmental factors adversely affecting food security. The seed germination stage is critical to ensuring the growth and productivity of soybeans in soils prone to drought conditions. We here examined the genetic diversity and drought-tolerance phenotypes of 410 accessions of a germplasm diversity panel for soybean and conducted quantitative genetics analyses to identify loci associated with the drought-tolerance of seedlings. Results We uncovered significant differences among the diverse genotypes for 4 growth indices and 5 drought-tolerance indices, which revealed abundant variation among genotypes, upon drought stress, and for genotype × treatment effects. We also used 158,327 SNP markers, and performed GWAS for the drought-related traits. Our data met the conditions (PCA + K) for using a mixed linear model in TASSEL, and we thusly identified 26 SNPs associated with drought tolerance indices for germination stage soybean plants. These were distributed across 10 soybean chromosomes, and these explain 5.19–9.66% of the observed phenotypic variation. Nine SNP sites, including for example Gm20_34956219 and Gm20_34956219, were associated with two or more phenotypic indices, and there were nine SNP markers located in or adjacent to (within 500 kb) previously reported drought tolerance QTLs. These SNP led to our identification of 41 candidate genes related to drought tolerance in the germination stage. Conclusion The results of our study contribute to a deeper understanding of the genetic mechanisms underlying drought tolerance in soybeans at the germination stage, thereby providing a molecular basis for identifying useful soybean germplasm for breeding new drought-tolerant varieties.

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