scholarly journals Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing

2021 ◽  
Author(s):  
Nisar Uddin ◽  
Harshraj Shinde ◽  
Kiflu Tesfamicael ◽  
Niaz Ali ◽  
Penny J Tricker ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Height ◽  
Genome Wide Association Study ◽  
Polymorphic Information Content ◽  
Genotyping By Sequencing ◽  
Fruit Weight ◽  
Ziziphus Mauritiana ◽  
Principal Coordinates ◽  
A Genome ◽  
Jujube Fruit

Ziziphus are economically and nutritionally important fruiting plants that were domesticated in China around 7000 years ago. We identified genetic diversity in 141 accessions of four, different species collected in Pakistan and in China, including wild species of Ziziphus mauritiana, Z. nummularia and Z. oxyphllya, and both wild and domesticated Z. jujuba Mill. Population structure, phylogenetic analysis and principal coordinates analysis based on 10,889 high-quality SNPs derived from genotyping-by-sequencing indicated that the accessions clustered into two major groups. The wild Pakistani Z. jujuba and Z. nummularia exhibited higher genetic diversity and polymorphic information content (0.37 and 0.23 respectively) than other species. We further conducted a genome-wide association study and discovered six highly significant marker-trait associations for fruit weight and plant height in this population. Our study provides important information for future breeding of Ziziphus species.

scholarly journals Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Abate Mekonnen Solomon ◽  
Tae-Gun Kim ◽  
Koeun Han ◽  
Hea-Young Lee ◽  
Abhinandan Patil ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Dominant Gene ◽  
Germplasm Collection ◽  
Region Of Interest ◽  
Genotyping By Sequencing ◽  
Fruit Weight ◽  
Chromosome 12 ◽  
Single Quantitative Trait Locus ◽  
A Genome ◽  
Capsicum Spp

The orientation of fruits is a distinguishing morphological feature of pepper (Capsicum spp.) varieties. The pendent (downward curved) growth of the fruit stalks, known as pedicels, is highly correlated with fruit weight and pedicel length. A previous genetic analysis revealed that the pendent fruit orientation is governed by a dominant gene, and incomplete inheritance is also observed in some Capsicum accessions. To identify and localize this gene, a single quantitative trait locus (QTL) analysis was performed on one F2 and two recombinant inbred line (RIL) populations, and a genome-wide association study (GWAS) was performed using a core collection. Common QTL regions associated with fruit orientation were detected on chromosome 12. A total of 187,966 SNPs were identified in a genotyping-by-sequencing (GBS) for GWAS analysis of 196 Capsicum annuum, 25 Capsicum baccatum, 21 Capsicum chinense, and 14 Capsicum frutescens accessions, representing the germplasm collection of South Korea. The results of these analyses enabled us to narrow down the CapUp region of interest to 200–250 Mbp on chromosome 12. Seven candidate genes were found to be located between two markers that were completely cosegregated with the fruit orientation phenotype. The findings and markers developed in this study will be helpful for additional understanding of pepper fruit development and breeding for fruit orientation.

scholarly journals Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ali Muhammad ◽  
Jianguo Li ◽  
Weichen Hu ◽  
Jinsheng Yu ◽  
Shahid Ullah Khan ◽  
...  
Keyword(s):  
Plant Height ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Significant Snps ◽  
Complex Trait ◽  
Leaf Length ◽  
Candidate Snps ◽  
A Genome ◽  
Multiple Environments ◽  
Architectural Traits

AbstractWheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.

scholarly journals GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 803 ◽  
Author(s):  
Wang ◽  
Yan ◽  
Li ◽  
Li ◽  
Zhao ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Market Demand ◽  
Oil Crops ◽  
A Genome ◽  
Genomic Regions

Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

scholarly journals Assessment of Genetic Diversity and Population Structure of Tunisian Barley Accessions (Hordeum vulgare L.) Using SSR Markers

2020 ◽  
Vol 73 (4) ◽  
Author(s):  
Salem Marzougui ◽  
Mohamed Kharrat ◽  
Mongi Ben Younes
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Hordeum Vulgare L ◽  
Software Analysis ◽  
Average Value ◽  
Allele Number ◽  
Cultivar Development ◽  
Principal Coordinates ◽  
Ssr Loci

In barley breeding programs, information about genetic dissimilarity and population structure is very important for genetic diversity conservation and new cultivar development. This study aimed to evaluate the genetic variation in Tunisian barley accessions (<em>Hordeum</em><em> </em><em>vulgare </em>L.) based on simple sequence repeat (SSR). A total of 89 alleles were detected at 26 SSR loci. The allele number per locus ranged from two to five, with an average of 3.4 alleles per locus detected from 32 barley accessions, and the average value of polymorphic information content was 0.45. A cluster analysis based on genetic similarity was performed, and the 32 barley resources were classified into five groups. Principal coordinates (PCoA) explained 12.5% and 9.3% of the total variation, and the PCoA was largely consistent with the results of cluster separation of STRUCTURE software analysis. The analysis of genetic diversity in barley collection will facilitate cultivar development and effective use of genetic resources.

scholarly journals Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

2021 ◽  
Author(s):  
Dong Cao ◽  
Dongxia Wang ◽  
Shiming Li ◽  
Yun Li ◽  
Ming Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Energy Crop ◽  
Hexaploid Triticale ◽  
Genome Wide ◽  
Genetic Mechanisms

Abstract Key message The genetic diversity and loci underlying agronomic traits were analysed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.Abstract Triticale (×Triticosecale Wittmack) is an economically important grain-forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.

scholarly journals Genome-Wide Association Study Reveals Genetic Architecture of Septoria Tritici Blotch Resistance in a Historic Landrace Collection

2021 ◽  
Author(s):  
Anik Dutta ◽  
Daniel Croll ◽  
Bruce A. McDonald ◽  
Simon G. Krattinger
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Variability ◽  
Genome Wide Association ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Genome Wide ◽  
A Genome ◽  
Wheat Landraces

Abstract Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is a major constraint in global wheat production. The lack of genetic diversity in modern elite wheat cultivars largely hinders the improvement of STB resistance. Wheat landraces are reservoirs of untapped genetic diversity, which can be exploited to find novel STB resistance genes or alleles. Here, we characterized 188 Swiss wheat landraces for resistance to STB using four Swiss Z. tritici isolates. We used a genome-wide association study (GWAS) to identify genetic variants associated with the amount of lesion and pycnidia production by the fungus. The majority of the landraces were highly resistant for both traits to the isolate 1E4, indicating a gene-for-gene relationship, while higher phenotypic variability was observed against other isolates. GWAS detected a significant SNP on chromosome 3A that was associated with both traits in the isolate 1E4. The resistance response against 1E4 was likely controlled by the Stb6 gene. Sanger sequencing revealed that the majority of these ~100-year-old landraces carry the Stb6 resistance allele. This indicates the importance of this gene in Switzerland during the early 1900s for disease control in the field. Our study demonstrates the importance of characterizing historic landrace collections for STB resistance to provide valuable information on resistance variability and contributing alleles. This will help breeders in the future to make decisions on integrating such germplasms in STB resistance breeding.

scholarly journals Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Shijing Feng ◽  
Zhenshan Liu ◽  
Yang Hu ◽  
Jieyun Tian ◽  
Tuxi Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Gansu Province ◽  
Climatic Oscillations ◽  
Genome Wide ◽  
A Genome ◽  
Wild Accessions

Abstract Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

scholarly journals High SNP diversity in the non-toxic indigenous Jatropha curcas germplasm widens the potential of this upcoming major biofuel crop species

2019 ◽  
Vol 124 (4) ◽  
pp. 645-652 ◽  
Author(s):  
K Vandepitte ◽  
O A Valdés-Rodríquez ◽  
O Sánchez-Sánchez ◽  
H De Kort ◽  
J Martinez-Herrera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Jatropha Curcas ◽  
Genome Wide Association Study ◽  
Animal Feed ◽  
Genomic Research ◽  
Breeding Value ◽  
Great Promise ◽  
Crop Species ◽  
Southern Mexico ◽  
A Genome

Abstract Background and Aims Jatropha curcas (jatropha) is an oil crop cultivated in (sub)tropical regions around the world, and holds great promise as a renewable energy source. However, efforts to fully commercialize jatropha are currently hampered by the lack of genetic diversity in the extant breeding germplasm, and by the toxicity of its seeds meaning that its seed cake cannot be used as a protein source in animal feed, among other constraints. In Mexico, the species’ native range, there are jatropha plants whose seeds are used to prepare traditional meals. This non-toxic jatropha ‘type’ is considered to harbour low genetic variation due to a presumed domestication bottleneck and therefore to be of limited breeding value; yet, very little is known regarding its origin and genetic diversity. Methods Using genotyping-by-sequencing (GBS), we extensively genotyped both indigenous toxic and non-toxic jatropha collected along roads and home gardens throughout southern Mexico. Key Results Single nucleotide polymorphism diversity in non-toxic jatropha is relatively high, particularly in northern Veracruz state, the probable origin of this germplasm. Genetic differences between toxic and non-toxic indigenous genotypes are overall quite small. A a genome-wide association study supported a genomic region (on LG 8, scaffold NW_012130064), probably involved in the suppression of seed toxicity. Conclusions Conservation actions are urgently needed to preserve this non-toxic indigenous, relatively wild germplasm, having potential as a fuel feedstock, animal feed and food source among other uses. More generally, this work demonstrates the value of conservation genomic research on the indigenous gene pool of economically important plant species.

scholarly journals Genome wide association study of plant height and tiller number in hulless barley

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260723
Author(s):  
Yixiong Bai ◽  
Xiaohong Zhao ◽  
Xiaohua Yao ◽  
Youhua Yao ◽  
Likun An ◽  
...  
Keyword(s):  
Association Study ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Tiller Number ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Hulless Barley ◽  
Genome Wide ◽  
A Genome

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.

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