scholarly journals Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 518 ◽  
Author(s):  
Ana Campa ◽  
Ester Murube ◽  
Juan José Ferreira
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Association Studies ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Gene Pools ◽  
Genome Wide Association Studies ◽  
Snap Bean ◽  
Diversity Panel ◽  
Main Gene

A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, so this panel can be considered to be representative of the Spanish diversity for this species. The panel was characterized by 3099 single-nucleotide polymorphism markers obtained through genotyping-by-sequencing, which revealed a wide genetic diversity and a low level of redundant material within the panel. Structure, cluster, and principal component analyses revealed the presence of two main subpopulations corresponding to the two main gene pools identified in common bean, the Andean and Mesoamerican pools, although most lines (70%) were associated with the Andean gene pool. Lines showing recombination between the two gene pools were also observed, most of them showing useful for snap bean consumption, which suggests that both gene pools were probably used in the breeding of snap bean cultivars. The usefulness of this panel for genome-wide association studies was tested by conducting association mapping for determinacy. Significant marker–trait associations were found on chromosome Pv01, involving the gene Phvul.001G189200, which was identified as a candidate gene for determinacy in the common bean.

scholarly journals Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jessica Delfini ◽  
Vânia Moda-Cirino ◽  
José dos Santos Neto ◽  
Paulo Maurício Ruas ◽  
Gustavo César Sant’Ana ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Pool ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Gene Pools ◽  
Genome Wide Association Studies ◽  
Mesoamerican Gene Pool ◽  
Diversity Panel

AbstractBrazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.

scholarly journals Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11593
Author(s):  
Vipin Tomar ◽  
Guriqbal Singh Dhillon ◽  
Daljit Singh ◽  
Ravi Prakash Singh ◽  
Jesse Poland ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Association Studies ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Genome Wide Association Studies ◽  
Breeding Lines ◽  
Structure Information

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

scholarly journals Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1298
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Sérgio Augusto Morais Carbonell ◽  
Alisson Fernando Chiorato ◽  
Qijian Song ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Diversity ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

scholarly journals Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies

2020 ◽  
Vol 61 (5) ◽  
pp. 922-932 ◽  
Author(s):  
N Tanaka ◽  
M Shenton ◽  
Y Kawahara ◽  
M Kumagai ◽  
H Sakai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Sequence Data ◽  
Association Studies ◽  
Crop Improvement ◽  
Heading Date ◽  
Principal Component ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Population Structure Analysis

Abstract Genebanks provide access to diverse materials for crop improvement. To utilize and evaluate them effectively, core collections, such as the World Rice Core Collection (WRC) in the Genebank at the National Agriculture and Food Research Organization, have been developed. Because the WRC consists of 69 accessions with a high degree of genetic diversity, it has been used for >300 projects. To allow deeper investigation of existing WRC data and to further promote research using Genebank rice accessions, we performed whole-genome resequencing of these 69 accessions, examining their sequence variation by mapping against the Oryza sativa ssp. japonica Nipponbare genome. We obtained a total of 2,805,329 single nucleotide polymorphisms (SNPs) and 357,639 insertion–deletions. Based on the principal component analysis and population structure analysis of these data, the WRC can be classified into three major groups. We applied TASUKE, a multiple genome browser to visualize the different WRC genome sequences, and classified haplotype groups of genes affecting seed characteristics and heading date. TASUKE thus provides access to WRC genotypes as a tool for reverse genetics. We examined the suitability of the compact WRC population for genome-wide association studies (GWASs). Heading date, affected by a large number of quantitative trait loci (QTLs), was not associated with known genes, but several seed-related phenotypes were associated with known genes. Thus, for QTLs of strong effect, the compact WRC performed well in GWAS. This information enables us to understand genetic diversity in 37,000 rice accessions maintained in the Genebank and to find genes associated with different phenotypes. The sequence data have been deposited in DNA Data Bank of Japan Sequence Read Archive (DRA) (Supplementary Table S1).

scholarly journals Structure of genetic diversity and genome-wide association studies of bean fly (Ophiomyia spencerella) resistance in common bean

Euphytica ◽  
2021 ◽  
Vol 217 (12) ◽  
Author(s):  
Pascal P. Okwiri Ojwang ◽  
Tilly Eldridge ◽  
Pilar Corredor-Moreno ◽  
Vincent Njung’e
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Association Studies ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Eastern Africa ◽  
Genome Wide Association Studies ◽  
Ophiomyia Spencerella ◽  
Genome Wide ◽  
Bean Fly

AbstractEastern Africa is a significant region of common bean (Phaseolus vulgaris L.) production and genetic diversity. Insect pests are a major biotic constraint in subsistence crop production systems. Bean fly (Ophiomyia spencerella) is a serious pest of beans in eastern Africa highlands. Breeding efforts focus on combining adaptability traits with user preferred seed types. However, lack of information on molecular markers linked to genes modulating bean fly resistance has slowed breeding progress. The objectives were to: (i) characterize genetic diversity and uncover putative bean fly resistant genotypes within diverse seed types and market classes and (ii) identify genomic regions controlling bean fly resistance using genome-wide association analysis (GWAS). A set of 276 diverse genotypes comprising local landraces and varieties from Kenya alongside introductions from International Centre for Tropical Agriculture (CIAT), were assembled. The germplasm represented varied bean production ecologies and seed types. Genetic diversity conforming to Andean and Mesoamerican genepools was established. Out of 276 genotypes evaluated, 150 were Andean, 74 were Mesoamerican and 52 were admixed. Twenty-two genotypes were resistant to bean fly. Association mapping results for stem damage score and plant mortality identified six significant single-nucleotide polymorphisms (SNPs) on chromosomes Pv01 and Pv09. The most significant SNP marker was 12 kilobases downstream of Phvul.001G074900 gene with LOD score > 4.0 hence in linkage disequilibrium with the postulated gene. The identified candidate gene is pleiotropic and modulates both flowering time and plant responses to stress. These findings are a key step towards marker-enabled breeding in common bean for sub-Saharan Africa.

scholarly journals Genome-level diversification of eight ancient tea populations in the Guizhou and Yunnan regions identifies candidate genes for core agronomic traits

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Litang Lu ◽  
Hufang Chen ◽  
Xiaojing Wang ◽  
Yichen Zhao ◽  
Xinzhuan Yao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Agronomic Traits ◽  
Association Studies ◽  
Functional Characterization ◽  
Principal Component ◽  
Tea Plant ◽  
Guizhou Province ◽  
Genome Wide Association Studies ◽  
Tea Plants

AbstractThe ancient tea plant, as a precious natural resource and source of tea plant genetic diversity, is of great value for studying the evolutionary mechanism, diversification, and domestication of plants. The overall genetic diversity among ancient tea plants and the genetic changes that occurred during natural selection remain poorly understood. Here, we report the genome resequencing of eight different groups consisting of 120 ancient tea plants: six groups from Guizhou Province and two groups from Yunnan Province. Based on the 8,082,370 identified high-quality SNPs, we constructed phylogenetic relationships, assessed population structure, and performed genome-wide association studies (GWAS). Our phylogenetic analysis showed that the 120 ancient tea plants were mainly clustered into three groups and five single branches, which is consistent with the results of principal component analysis (PCA). Ancient tea plants were further divided into seven subpopulations based on genetic structure analysis. Moreover, it was found that the variation in ancient tea plants was not reduced by pressure from the external natural environment or artificial breeding (nonsynonymous/synonymous = 1.05). By integrating GWAS, selection signals, and gene function prediction, four candidate genes were significantly associated with three leaf traits, and two candidate genes were significantly associated with plant type. These candidate genes can be used for further functional characterization and genetic improvement of tea plants.

scholarly journals Molecular and genetic analysis of defensive responses of Brassica juncea – B. fruticulosa introgression lines to Sclerotinia infection

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chhaya Atri ◽  
Javed Akhatar ◽  
Mehak Gupta ◽  
Neha Gupta ◽  
Anna Goyal ◽  
...  
Keyword(s):  
Association Studies ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Genomic Region ◽  
Introgression Lines ◽  
Stem Rot ◽  
Gene Pools ◽  
Genome Wide Association Studies ◽  
Major Disease ◽  
Defensive Responses

AbstractSclerotinia stem rot caused by Sclerotinia sclerotiorum is a major disease of crop brassicas, with inadequate variation for resistance in primary gene pools. We utilized a wild Brassicaceae species with excellent resistance against stem rot to develop a set of B. juncea - B. fruticulosa introgression lines (ILs). These were assessed for resistance using a highly reproducible stem inoculation technique against a virulent pathogen isolate. Over 40% of ILs showed higher levels of resistance. IL-43, IL-175, IL-215, IL-223 and IL-277 were most resistant ILs over three crop seasons. Sequence reads (21x) from the three most diverse ILs were then used to create B. juncea pseudomolecules, by replacing SNPs of reference B. juncea with those of re-sequenced ILs. Genotyping by sequencing (GBS) was also carried out for 88 ILs. Resultant sequence tags were then mapped on to the B. juncea pseudomolecules, and SNP genotypes prepared for each IL. Genome wide association studies helped to map resistance responses to stem rot. A total of 13 significant loci were identified on seven B. juncea chromosomes (A01, A03, A04, A05, A08, A09 and B05). Annotation of the genomic region around identified SNPs allowed identification of 20 candidate genes belonging to major disease resistance protein families, including TIR-NBS-LRR class, Chitinase, Malectin/receptor-like protein kinase, defensin-like (DEFL), desulfoglucosinolate sulfotransferase protein and lipoxygenase. A majority of the significant SNPs could be validated using whole genome sequences (21x) from five advanced generation lines being bred for Sclerotinia resistance as compared to three susceptible B. juncea germplasm lines. Our findings not only provide critical new understanding of the defensive pathway of B. fruticulosa resistance, but will also enable development of marker candidates for assisted transfer of introgressed resistant loci in to agronomically superior cultivars of crop Brassica.

scholarly journals Genetic Diversity and Population Differentiation of Pinus koraiensis in China

Horticulturae ◽  
2021 ◽  
Vol 7 (5) ◽  
pp. 104
Author(s):  
Xiang Li ◽  
Minghui Zhao ◽  
Yujin Xu ◽  
Yan Li ◽  
Mulualem Tigabu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Genetic Information ◽  
Expressed Sequence Tag ◽  
Association Studies ◽  
Genetic Erosion ◽  
Principal Component ◽  
Pinus Koraiensis ◽  
Genome Wide Association Studies ◽  
Ecological Value

Pinus koraiensis is a well-known precious tree species in East Asia with high economic, ornamental and ecological value. More than fifty percent of the P. koraiensis forests in the world are distributed in northeast China, a region with abundant germplasm resources. However, these natural P. koraiensis sources are in danger of genetic erosion caused by continuous climate changes, natural disturbances such as wildfire and frequent human activity. Little work has been conducted on the population genetic structure and genetic differentiation of P. koraiensis in China because of the lack of genetic information. In this study, 480 P. koraiensis individuals from 16 natural populations were sampled and genotyped. Fifteen polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to evaluate genetic diversity, population structure and differentiation in P. koraiensis. Analysis of molecular variance (AMOVA) of the EST-SSR marker data showed that 33% of the total genetic variation was among populations and 67% was within populations. A high level of genetic diversity was found across the P. koraiensis populations, and the highest levels of genetic diversity were found in HH, ZH, LS and TL populations. Moreover, pairwise Fst values revealed significant genetic differentiation among populations (mean Fst = 0.177). According to the results of the STRUCTURE and Neighbor-joining (NJ) tree analyses and principal component analysis (PCA), the studied geographical populations cluster into two genetic clusters: cluster 1 from Xiaoxinganling Mountains and cluster 2 from Changbaishan Mountains. These results are consistent with the geographical distributions of the populations. The results provide new genetic information for future genome-wide association studies (GWAS), marker-assisted selection (MAS) and genomic selection (GS) in natural P. koraiensis breeding programs and can aid the development of conservation and management strategies for this valuable conifer species.

scholarly journals Molecular Characterization of Global Finger Millet (Eleusine coracana, L. Gaertn) germplasm Reaction to Striga in Kenya

2018 ◽  
pp. 1-14
Author(s):  
Sirengo Peter Nyongesa ◽  
Wamalwa Dennis Simiyu ◽  
Oduor Chrispus ◽  
Odeny Damaris Achieng ◽  
Dangasuk Otto George
Keyword(s):  
Finger Millet ◽  
Association Studies ◽  
Block Design ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Eleusine Coracana ◽  
Striga Hermonthica ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Striga Resistance

Finger millet (Eleusine coracana, L. Gaertn) is an important food crop in Africa and Asia. The parasitic weed Striga hermonthica (Del.) Benth limits finger millet production through reduced yield in agro-ecologies where they exist. The damage of Striga to cereal crops is more severe under drought and low soil fertility. This study aims to determine genetic basis for reaction to Striga hermonthica among the selected germplasm of finger millets through genotyping by sequencing (GBS). One hundred finger millet genotypes were evaluated for reaction to Striga hermonthica infestation under field conditions at Alupe and Kibos in Western Kenya. The experiment was laid out in a randomized complete block design (RCBD) consisting of 10 x 10 square (triple lattice) under Striga (inoculated) and no Striga conditions and plant growth monitored to maturity after 110 days. All genotypes were genotyped by genotyping by sequencing (GBS) and data analyzed using the non-reference based Universal Network Enabled Analysis Kit (UNEAK) pipeline. Genome wide association studies (GWAS) were done to establish the association of detected Single Nucleotide Polymorphisms (SNPs) with Striga reaction based on field results. In molecular analysis 117,542 SNPs from raw GBS data used in GWAS revealed that markers TP 85424 and TP 88244 were associated with Striga resistance in the 95 genotypes. Principal Component Analysis revealed that the first and third component axes accounted for 2.5 and 8% of total variance respectively and the genotypes were distributed according to their reaction to Striga weed. Genetic diversity analysis grouped the 95 accessions into three major clusters containing; 32 (A), 56 (B), and 7 (C) genotypes.  All finger millet genotypes that showed high resistance to Striga in the field were from cluster B while the most susceptible genotypes were from clusters A and C. Results revealed genetic variation for Striga resistance in cultivated finger millet genotypes and hence the possibility of marker –assisted breeding for resistance to Striga.

scholarly journals Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Xin Wang ◽  
Kaori Ando ◽  
Shan Wu ◽  
Umesh K. Reddy ◽  
Prabin Tamang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Future Research ◽  
Genome Wide Association Studies ◽  
The Core ◽  
Plant Germplasm ◽  
National Plant Germplasm System ◽  
The U.S

AbstractMelon (C. melo L.) is an economically important vegetable crop cultivated worldwide. The melon collection in the U.S. National Plant Germplasm System (NPGS) is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding. Here we use the genotyping-by-sequencing (GBS) technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist. Population structure and genetic diversity analyses suggested that C. melo ssp. melo was firstly introduced from the centers of origin, Indian and Pakistan, to Central and West Asia, and then brought to Europe and Americas. C. melo ssp. melo from East Asia was likely derived from C. melo ssp. agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp. melo accessions from other geographic regions. We developed a core collection of 383 accessions capturing more than 98% of genetic variation in the germplasm, providing a publicly accessible collection for future research and genomics-assisted breeding of melon. Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection. Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits. This study provides insights into melon origin and domestication, and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

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