scholarly journals Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dennis N. Lozada ◽  
Madhav Bhatta ◽  
Danise Coon ◽  
Paul W. Bosland
Keyword(s):  
Genetic Diversity ◽  
New Mexico ◽  
Genetic Improvement ◽  
The United States ◽  
Snp Markers ◽  
Single Nucleotide ◽  
Chile Pepper ◽  
New Mexican ◽  
Selection For ◽  
Chile Peppers

Abstract Background Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Results A GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper cultivars showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K = 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08 %). Extensive LD decay (~ 5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genome wide association studies for different traits in New Mexican type chile peppers. Tajima’s D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm. Conclusions Genetic diversity among New Mexican chile peppers was evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.

scholarly journals Single Nucleotide Polymorphisms Reveal Genetic Diversity in New Mexican Chile Peppers (Capsicum Spp.) 

2021 ◽  
Author(s):  
Dennis N. Lozada ◽  
Madhav Bhatta ◽  
Danise Coon ◽  
Paul W. Bosland
Keyword(s):  
Genetic Diversity ◽  
New Mexico ◽  
Genetic Improvement ◽  
The United States ◽  
Snp Markers ◽  
Single Nucleotide ◽  
Chile Pepper ◽  
New Mexican ◽  
Selection For ◽  
Chile Peppers

Abstract Background: Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Results: A GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper varieties showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K= 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08%). Extensive LD decay (~5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genomewide association studies for different traits in New Mexican type chile peppers. Tajima’s D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm. Conclusions: Analysis of genetic diversity among New Mexican chile peppers were evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

2021 ◽  
Vol 19 (1) ◽  
pp. 20-28
Author(s):  
Abush Tesfaye Abebe ◽  
Adesike Oladoyin Kolawole ◽  
Nnanna Unachukwu ◽  
Godfree Chigeza ◽  
Hailu Tefera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Glycine Max ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Lines ◽  
Soybean Germplasm ◽  
Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

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.

scholarly journals Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers

2020 ◽  
Vol 56 (No. 2) ◽  
pp. 62-70 ◽  
Author(s):  
Shahril Ab Razak ◽  
Nor Helwa Ezzah Nor Azman ◽  
Rahiniza Kamaruzaman ◽  
Shamsul Amri Saidon ◽  
Muhammad Fairuz Mohd Yusof ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Crop Improvement ◽  
Snp Markers ◽  
Group Method ◽  
Chromosome 11 ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
K Value

Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of the SNPs per chromosome revealed that the average of the polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. The genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups. The analysis was supported by the findings from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2, followed by K = 4. The pairwise genetic distance of the shared alleles showed that the value ranged from 0.000 (MR159–MR167) to 0.723 (MRIA–Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

Genetic diversity and parentage of Tunisian wild and cultivated grapevines (Vitis vinifera L.) as revealed by single nucleotide polymorphism (SNP) markers

2014 ◽  
Vol 10 (4) ◽  
pp. 1103-1112 ◽  
Author(s):  
Sana Ghaffari ◽  
Nejib Hasnaoui ◽  
Lalla Hasna Zinelabidine ◽  
Ali Ferchichi ◽  
José M. Martínez-Zapater ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Vitis Vinifera ◽  
Snp Markers ◽  
Vitis Vinifera L ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Wang ◽  
Xiaohua Wu ◽  
Yanwei Li ◽  
Zishan Feng ◽  
Zihan Mu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Snp Markers ◽  
Bottle Gourd ◽  
Snp Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Core ◽  
Germplasm Collections ◽  
Diversity Assessment

Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.

scholarly journals (275) Genetic Relationship of Fruiting-mei (Prunus mume Sieb. et Zucc.) Cultivars Evaluated by AFLP and SNP Markers

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 1036A-1036
Author(s):  
Jinggui Fang ◽  
Tal Twito ◽  
Zhen Zhang ◽  
Chih Cheng T. Chao
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationship ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Prunus Mume ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Past ◽  
China And Japan ◽  
Relationship Of

The genetic relationship among 50 fruiting-mei (Prunus mume Sieb. et Zucc.) cultivars from China and Japan was investigated using 767 amplified fragment length polymorphism (AFLP) and 103 single nucleotide polymorphism (SNP) markers. The polymorphism among the cultivars was 69.77% based on EcoR I + Mse I AFLP primer pairs. The sequence alignment of 11 group sequences derived from 50 samples yielded 103 SNPs with a total length of 3683-bp genomic sequences. Among these SNPs, 73 were heterozygous in the loci of different cultivars. The SNP distribution were: 58% transition, 40% transversion, and 2% InDels. There was also one tri-nucleotide deletion. Both AFLP and SNP allowed the evaluation of genetic diversity of these 50 fruiting-mei cultivars; however, the two derived cladograms have some differences: 1) all the cultivars formed two sub-clusters (1A and 1B) within cladogram based on AFLP polymorphisms, and there were three sub-clusters (2A, 2B and 2C) formed in the cladogram based on SNP polymorphisms; and 2) most cultivars from G-F, Y-H-S regions and Japan are grouped in cluster 1A and 18 (78.26%) out of 23 cultivars from J-Z origin are grouped in cluster 1B in the cladogram generated based on AFLP polymorphisms. The results show cultivars from Japan are clustered within cultivars from China and supports the hypothesis that fruitingmei in Japan was introduced from China in the past. Cultivars from J-Z region of China have higher genetic similarities. Cultivars from G-F and Y-S-H regions have lower genetic similarities and suggest more germplasm exchanges in the past.

scholarly journals Development and Application of Novel Indel Markers in Flax (Linum Usitatissimum L.) Through Whole-genome Re-sequencing

2021 ◽  
Author(s):  
Hui Jiang ◽  
Gen Pan ◽  
Touming Liu ◽  
Li Chang ◽  
Siqi Huang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Snp Markers ◽  
Diversity Analysis ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genetic Diversity Analysis ◽  
Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

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