Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties

Abstract Background The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001). Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

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Genotyping pepper varieties using Target SNP-seq reveals that population structure clusters according to fruit shape

10.21203/rs.2.10821/v1 ◽

2019 ◽

Author(s):

Heshan Du ◽

Jingjing Yang ◽

Bin Chen ◽

Xiaofen Zhang ◽

Jian Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relatedness ◽

Principal Component ◽

Randomization Test ◽

Fruit Shape ◽

Variety Identification ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Chromosome 11 ◽

Multiplex Amplification

Abstract Background The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has characterized the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of single-nucleotide polymorphisms (SNPs) was created that consisted of 97 perfect SNPs, which were identified using re-sequencing data from 35 diverse C. annuum lines. Based on this panel, a Target SNP-seq was designed that combined the multiplex amplification of the perfect SNPs with Illumina sequencing to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content (PIC), observed heterozygosity (Ho), expected heterozygosity (He), and minor allele frequency (MAF), which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape; blocky, long horn, short horn, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn, linear, and blocky-fruited populations. A set of 35 core SNPs were then used as KASPar markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis (PCA) and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Notably, two SNP loci, CaSNP118 and CaSNP053, which are located on chromosome 11 and 6 were significantly associated with fruit shape (p < 1.0 × 10 -4) Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of the pepper varieties is significantly influenced by breeding programs focused on fruit shape.

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

Plants ◽

10.3390/plants9091190 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1190 ◽

Cited By ~ 1

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

10.21203/rs.3.rs-700179/v2 ◽

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

10.20944/preprints202011.0577.v1 ◽

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 × 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.

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Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs

PeerJ ◽

10.7717/peerj.8009 ◽

2019 ◽

Vol 7 ◽

pp. e8009

Author(s):

Yu Lin ◽

Qianzi Tang ◽

Yan Li ◽

Mengnan He ◽

Long Jin ◽

...

Keyword(s):

Principal Component ◽

Snp Markers ◽

Specific Pattern ◽

Whole Genome Sequencing Data ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Heterozygous Snps ◽

Specific Expression ◽

Origin Effects ◽

Crossbred Pigs

Crossbreeding is widely used aimed at improving crossbred performance for poultry and livestock. Alleles that are specific to different purebreds will yield a large number of heterozygous single-nucleotide polymorphisms (SNPs) in crossbred individuals, which are supposed to have the power to alter gene function or regulate gene expression. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is generally used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, little is known about the breed-of-origin effects from purebreds on DLY pigs. In this study, we first estimated the distribution of heterozygous SNPs in three kinds of three-way crossbred pigs via whole genome sequencing data originated from three purebreds. The result suggested that DLY is a more effective strategy for three-way crossbreeding as it could yield more stably inherited heterozygous SNPs. We then sequenced a DLY pig family and identified 95, 79, 132 and 42 allele-specific expression (ASE) genes in adipose, heart, liver and skeletal muscle, respectively. Principal component analysis and unrestricted clustering analyses revealed the tissue-specific pattern of ASE genes, indicating the potential roles of ASE genes for development of DLY pigs. In summary, our findings provided a lot of candidate SNP markers and ASE genes for DLY three-way crossbreeding system, which may be valuable for pig breeding and production in the future.

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Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

10.21203/rs.3.rs-700179/v1 ◽

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

Genes ◽

10.3390/genes12071042 ◽

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.

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Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

10.21203/rs.3.rs-779119/v1 ◽

2021 ◽

Author(s):

Guai-qiang Chai ◽

Yizhong Duan ◽

Peipei Jiao ◽

Zhongyu Du ◽

Furen Kang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Association Studies ◽

Natural Populations ◽

Principal Component ◽

Nucleotide Polymorphisms ◽

Future Design ◽

Ammopiptanthus Nanus ◽

Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

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Identification of SNP markers associated with antler growth rate in sika deer (Cervus nippon)

10.21203/rs.3.rs-44991/v1 ◽

2020 ◽

Author(s):

Pengfei Hu ◽

Yongyan Deng ◽

Hengxing Ba ◽

chunyi li

Keyword(s):

Growth Rate ◽

Sika Deer ◽

Cervus Nippon ◽

Snp Markers ◽

Whole Genome Sequencing Data ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Animal Genetic Resources ◽

Antler Growth ◽

Hardy Weinberg Equilibrium

Abstract Sika deer (Cervus nippon) constitutes one of the most valuable animal genetic resources in east Asia. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) from antler growth-related genes of sika deer. The whole genome sequencing data of sika deer were used to identify SNP markers. Among them, 31 SNPs from antler growth-related genes exhibited significant polymorphism using genotyping by mass spectrometry. The observed and expected heterozygosities were ranged from 0.147 to 0.997 and 0.201 to 0.500, respectively. Significant deviation from the Hardy-Weinberg equilibrium was observed in 6 loci. These findings provide effective molecular detection markers for the study of variation in antler growth rate of sika deer.

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Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa

Wellcome Open Research ◽

10.12688/wellcomeopenres.10784.2 ◽

2017 ◽

Vol 2 ◽

pp. 10 ◽

Cited By ~ 4

Author(s):

Irene Omedo ◽

Polycarp Mogeni ◽

Teun Bousema ◽

Kirk Rockett ◽

Alfred Amambua-Ngwa ◽

...

Keyword(s):

Genetic Relatedness ◽

Temporal Structure ◽

Principal Component ◽

Nucleotide Polymorphisms ◽

Homogeneous Population ◽

Space And Time ◽

Plasmodium Falciparum Parasite ◽

Spatio Temporal ◽

Parasite Populations ◽

The Relationship

Background: The first models of malaria transmission assumed a completely mixed and homogeneous population of parasites. Recent models include spatial heterogeneity and variably mixed populations. However, there are few empiric estimates of parasite mixing with which to parametize such models. Methods: Here we genotype 276 single nucleotide polymorphisms (SNPs) in 5199 P. falciparum isolates from two Kenyan sites (Kilifi county and Rachuonyo South district) and one Gambian site (Kombo coastal districts) to determine the spatio-temporal extent of parasite mixing, and use Principal Component Analysis (PCA) and linear regression to examine the relationship between genetic relatedness and distance in space and time for parasite pairs. Results: Using 107, 177 and 82 SNPs that were successfully genotyped in 133, 1602, and 1034 parasite isolates from The Gambia, Kilifi and Rachuonyo South district, respectively, we show that there are no discrete geographically restricted parasite sub-populations, but instead we see a diffuse spatio-temporal structure to parasite genotypes. Genetic relatedness of sample pairs is predicted by relatedness in space and time. Conclusions: Our findings suggest that targeted malaria control will benefit the surrounding community, but unfortunately also that emerging drug resistance will spread rapidly through the population.

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