scholarly journals Genetic Diversity And Population Structure of Indian Mustard (Brassica Juncea) Based On Morphological and Molecular Markers

2021 ◽  
Author(s):  
Prashant Yadav ◽  
Sushma Yadav ◽  
Anurag Mishra ◽  
Rajat Chaudhary ◽  
Arun Kumar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Indian Mustard ◽  
Leafy Vegetables ◽  
Dissimilarity Matrix ◽  
Phenotypic Data ◽  
Breeding Lines ◽  
Linkage Algorithm ◽  
Population Structure Analysis ◽  
Genetic Stocks

Abstract Rapeseed-mustard is one of the most important oilseed crops and providing a major source of edible oil in the world besides having other economic importance like leafy vegetables, ornamentals, and hedge crops. However, the genetic diversity present in the Brassica gene pool has not been investigated in detail. To address this problem, a study was conducted on 76 genotypes of B. juncea including cultivars, exotic lines, registered genetic stocks, advanced breeding lines, and germplasm lines. The genetic diversity was analyzed with the help of 50 polymorphic SSR and EST-SSR markers. For these genotype-marker combinations, a total of 126 alleles were amplified. Using molecular and phenotypic data, the dendrogram was constructed based on Jaccard’s similarity coefficient and Manhattan dissimilarity coefficient and linkage algorithm UPGMA. All the genotypes were grouped into 5 clusters based on their dissimilarity matrix. Population structure analysis grouped the genotypes in 8 clusters and various degrees of admixture was also observed. The grouping of genotypes appears effective as per their pedigree. The marker data was found more accurate to characterize the diversity and study the population structure than the quantitative trait data. The results of the present investigation will provide useful information for the identification of important alleles for future studies and pave the way to enhance genetic gains in Indian mustard.

Understanding genetic diversity, population structure and development of a core collection of Indian accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. and Nakai)

2020 ◽  
pp. 1-10
Author(s):  
Saheb Pal ◽  
Muttanna Revadi ◽  
RN Thontadarya ◽  
DC Lakshmana Reddy ◽  
B. Varalakshmi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Core Collection ◽  
Gene Diversity ◽  
Citrullus Lanatus ◽  
Population Analysis ◽  
Maximum Magnitude ◽  
Phenotypic Data ◽  
Genetic Base ◽  
Population Structure Analysis

Abstract Most of the modern-day improved watermelon varieties succumb to various biotic and abiotic stresses mainly because of their narrow genetic base. Insights into the genetic diversity and population structure are crucial for broadening the genetic base and improving the adaptive value. The present experiment was conducted to study the genetic diversity and population structure of a germplasm panel comprising 336 Citrullus sp. accessions. Another objective was to formulate a core collection of Indian Citrullus sp. accessions. Data from 23 highly polymorphic microsatellite markers were used for genetic diversity and population structure analysis while both molecular and phenotypic data from 17 traits were used to formulate the core set. The markers yielded a total of 69 alleles with an average of three alleles per locus. Initially, the accessions clustered into two populations and an admixture group. Intra-population analysis revealed three and two statistically distinct subpopulations in Pop I and Pop II, respectively. The exotic collections were predominant in Pop I-A, Pop II-A and Pop II-B while the Indian accessions were preponderant in Pop I-B and Pop I-C. Pop I-B recorded the maximum magnitude of gene diversity and the highest number of alleles. The well-adapted Indian landraces could be deployed in future watermelon improvement programmes. The formulated core collection (n = 46; 23.71% of the entire collection studied) would ease in maintenance of the diversity present among indigenous Citrullus sp. accessions; would ease trait search while exploring Indian diversity and can be pooled with other collection(s) to form a global core of watermelon.

scholarly journals Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 118
Author(s):  
Ljiljana Brbaklić ◽  
Dragana Trkulja ◽  
Sanja Mikić ◽  
Milan Mirosavljević ◽  
Vojislava Momčilović ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Hordeum Vulgare ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Breeding Period ◽  
Phenotypic Variance ◽  
Hordeum Vulgare L ◽  
Phenotypic Data ◽  
Breeding Material

Determination of genetic diversity and population structure of breeding material is an important prerequisite for discovering novel and valuable alleles aimed at crop improvement. This study’s main objective was to characterize genetic diversity and population structure of a collection representing a 40-year long historical period of barley (Hordeum vulgare L.) breeding, using microsatellites, pedigree, and phenotypic data. The set of 90 barley genotypes was phenotyped during three growing seasons and genotyped with 338 polymorphic alleles. The indicators of genetic diversity showed differentiation changes throughout the breeding periods. The population structure discriminated the breeding material into three distinctive groups. The principal coordinate analysis grouped the genotypes according to their growth habit and row type. An analysis of phenotypic variance (ANOVA) showed that almost all investigated traits varied significantly between row types, seasons, and breeding periods. A positive effect on yield progress during the 40-year long breeding period could be partly attributed to breeding for shorter plants, which reduced lodging and thus provided higher yield stability. The breeding material revealed a considerable diversity level based on microsatellite and phenotypic data without a tendency of genetic erosion throughout the breeding history and implied dynamic changes in genetic backgrounds, providing a great gene pool suitable for further barley improvement.

scholarly journals Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei Wang ◽  
Chunyan Ma ◽  
Longling Ouyang ◽  
Wei Chen ◽  
Ming Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Genetic Constitution ◽  
Southern Group ◽  
Population Structure Analysis ◽  
Lateolabrax Maculatus ◽  
Geographic Populations ◽  
Geographic Separation

AbstractIn order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei’s genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

Genetic diversity and population structure of the rice false smut pathogen Ustilaginoidea virens in Sichuan-Chongqing region

Plant Disease ◽  
2021 ◽  
Author(s):  
Anfei Fang ◽  
Zhuangyuan Fu ◽  
Zexiong Wang ◽  
Yuhang Fu ◽  
Yubao Qin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Resistance Breeding ◽  
Ustilaginoidea Virens ◽  
Breeding Lines ◽  
Rice False Smut ◽  
Geographical Populations ◽  
False Smut

Rice false smut caused by Ustilaginoidea virens is currently one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from SNP-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. The groups Ⅰ and Ⅵ were the largest including 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. AMOVA showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup. The UPGMA dendrogram and population structure revealed that the genetic composition of isolates collected from ST (Santai), NC (Nanchong), YC (Yongchuan), and WS (Wansheng) dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

scholarly journals Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1190 ◽  
Author(s):  
Eunju Seo ◽  
Kipoong Kim ◽  
Tae-Hwan Jun ◽  
Jinsil Choi ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Principal Component ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Useful Knowledge ◽  
Population Structure Analysis ◽  
Group 3 ◽  
Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

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