Genetic Diversity and Population Structure of Traditional Chinese Herb “Chai-Hu” Resources Using Genome-Wide SNPs Through Genotyping-By-Sequencing

Bupleurum (named “Chai-hu”) is an important traditional Chinese medicine resource in China. It has been widely used since ancient times and has antipyretic, analgesic and cholagogic functions, but there is little research on its genetic diversity. In this study, genotyping-by-sequencing (GBS) was used to detect SNP loci in 39 Bupleurum germplasm resources from different regions in China and analyse their genetic diversity. A total of 25.1 Gb of data was obtained by sequencing, with an average of 0.64 Gb per sample. After screening, 83898 high-quality SNPs were obtained. The results of genetic research were obtained by phylogenetic tree, principal component analysis and population structure analysis, and the 39 experimental materials were divided into three groups. The average observed heterozygosity and expected heterozygosity of Bupleurum populations were 0.24 and 0.17, respectively, indicating that Bupleurum populations from five different provinces had a low level of genetic diversity. Population nucleotide diversity analysis and analysis of molecular variance showed that the percentage of intrapopulation variation was 120.88%, while the percentage of interpopulation variation was only 2.46%. There was relative aggregation of Bupleurum samples with the same geographical origin, but the division of population structure was not completely correlated with sample origin. The results showed that the genetic diversity of the materials was low and that the genetic variation was narrow. This provides a good basis for the genetic breeding and protection of species diversity of Bupleurum.

Mapping of additive and epistatic QTLs linked to seed longevity in bread wheat (Triticum aestivum L.)

Plant genetic resources are stored and regenerated in > 1750 gene banks storing > 7,000,000 accessions. Since seeds are the primary storage units, research on seed longevity is of particular importance. Quantitative trait loci (QTL) analysis of 15 traits related to seed longevity and dormancy using 7584 high-quality SNPs recorded across 2 years and originated from five production years revealed a total of 46 additive QTLs. Exploration of the QTLs with epistatic effect resulted in the detection of 29 pairs of epistatic QTLs. To our information, this is only the second report of epistatic QTLs for seed longevity in bread wheat. We conclude that in addition to dense genetic maps, the epistatic interaction between loci should be considered to capture more variation which remained unnoticed in additive mapping.

Genome-Wide Association Analysis To Delineate High-Quality Snps For Seed Micronutrient Density In Chickpea (Cicer Arietinum L.)

Chickpea is the most important nutrient rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with 50K Cicer SNP array and trait phenotyped in two different environments for four seed micro-nutrients (Cu, Fe, Mn, and Zn). The trait data and high-throughput 50K SNP genotypic data was used for genome-wide association study (GWAS) that led the discovery of gene/QTLs for seed Cu, Fe, Mn, and Zn concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all the four micronutrient concentrations (P ≤ 0.05). The mean concentration of seed Fe, Zn, Cu, and Mn pooled over two-year data was 146.1 ppm, 45.9 ppm, 63.8 ppm and 27.0 ppm respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 MTAs, 5 were stable (consistently identified in different environments), 6 were major (explain more than 15% phenotypic variation for an individual trait) and 3 were both major and stable MTAs. The stable and major MTAs identified during the present study shall prove useful in molecular breeding programs aimed at enhancing seed nutrient density of chickpea.

Population structure and genetic diversity in common bean accessions from Northeast Brazil

Common bean is of great relevance for several countries, especially those located in tropical regions. Common bean in Brazil has a wide genetic diversity, which is used by breeders to improve this crop. In this study, we used GBS methodology to genotype common bean accessions from Northeast Brazil, and to study its population structure and genetic diversity. After a filtering process, we identified 30,529 high-quality SNPs distributed in 11 linkage groups. The number of SNPs per chromosome ranged from 1,731 to 3,853. The population structure analysis separated the accessions into two subpopulations, according to K=2, one subpopulation with 26 Andean and the other with 60 Middle American accessions. Considering K=3, Middle American accessions were divided into two subpopulations with presence of allele mixture between these two groups. Based on the PCA, we were able to verify a narrow genetic base of accessions belonging to the Andean gene pool, as well as a vast genetic diversity among the accessions from the Middle American gene pool. The knowledge on the genetic diversity among the accessions is of extreme importance to subsidize the common bean breeding programs in Northeast Brazil, and to explore the variability existing in cultivars adapted to the specific bioclimatic conditions.

Genetic diversity and population structure of sheep (Ovis aries) in Sichuan, China

Sichuan, China, has abundant genetic resources of sheep (Ovis aries). However, their genetic diversity and population structure have been less studied, especially at the genome-wide level. In the present study, we employed the specific-locus amplified fragment sequencing for identifying genome-wide single nucleotide polymorphisms (SNPs) among five breeds of sheep distributed in Sichuan, including three local pure breeds, one composite breed, and one exotic breed of White Suffolk. From 494 million clean paired-end reads, we obtained a total of 327,845 high-quality SNPs that were evenly distributed among all 27 chromosomes, with a transition/transversion ratio of 2.56. Based on this SNP panel, we found that the overall nucleotide diversity was 0.2284 for all five breeds, with the highest and lowest diversity observed in Mage sheep (0.2125) and Butuo Black (0.1963) sheep, respectively. Both Wright’s fixation index and Identity-by-State distance revealed that all individuals of Liangshan Semifine-wool, White Suffolk, and Butuo Black sheep were respectively clustered together, and the breeds could be separated from each other, whereas Jialuo and Mage sheep had the closest genetic relationship and could not be distinguished from each other. In conclusion, we provide a reference panel of genome-wide and high-quality SNPs in five sheep breeds in Sichuan, by which their genetic diversity and population structures were investigated.

SNP Development in Penaeus vannamei via Next-Generation Sequencing and DNA Pool Sequencing

Next-generation sequencing and pool sequencing have been widely used in SNP (single-nucleotide polymorphism) detection and population genetics research; however, there are few reports on SNPs related to the growth of Penaeus vannamei. The purpose of this study was to call SNPs from rapid-growing (RG) and slow-growing (SG) individuals’ transcriptomes and use DNA pool sequencing to assess the reliability of SNPs. Two parameters were applied to detect SNPs. One parameter was the p-values generated using Fisher’s exact test, which were used to calculate the significance of allele frequency differences between RG and SG. The other one was the AFI (minor allele frequency imbalance), which was defined to highlight the fold changes in MAF (minor allele frequency) values between RG and SG. There were 216,015 hypothetical SNPs, which were obtained based on the transcriptome data. Finally, 104 high-quality SNPs and 96,819 low-quality SNPs were predicted. Then, 18 high-quality SNPs and 17 low-quality SNPs were selected to assess the reliability of the detection process. Here, 72.22% (13/18) accuracy was achieved for high-quality SNPs, while only 52.94% (9/17) accuracy was achieved for low-quality SNPs. These SNPs enrich the data for population genetics studies of P. vannamei and may play a role in the development of SNP markers for future breeding studies.

Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)

Growth is one of the most important traits of an organism. For exploited species, this trait has ecological and evolutionary consequences as well as economical and conservation significance. Rapid changes in growth rate associated with anthropogenic stressors have been reported for several marine fishes, but little is known about the genetic basis of growth traits in teleosts. We used reduced genome representation data and genome-wide association approaches to identify growth-related genetic variation in the commercially, recreationally, and culturally important Australian snapper (Chrysophrys auratus, Sparidae). Based on 17,490 high-quality SNPs and 363 individuals representing extreme growth phenotypes from 15,000 fish of the same age and reared under identical conditions in a sea pen, we identified 100 unique candidates that were annotated to 51 proteins. We documented a complex polygenic nature of growth in the species that included several loci with small effects and a few loci with larger effects. Overall heritability was high (75.7%), reflected in the high accuracy of the genomic prediction for the phenotype (small vs large). Although the SNPs were distributed across the genome, most candidates (60%) clustered on chromosome 16, which also explains the largest proportion of heritability (16.4%). This study demonstrates that reduced genome representation SNPs and the right bioinformatic tools provide a cost-efficient approach to identify growth-related loci and to describe genomic architectures of complex quantitative traits. Our results help to inform captive aquaculture breeding programmes and are of relevance to monitor growth-related evolutionary shifts in wild populations in response to anthropogenic pressures.

DArT-based evaluation of soybean germplasm from Polish Gene Bank

Objective Soybean is an important plant used for food, feed and many industrial purposes. Interest in soybean breeding is growing in Central Europe, including Poland. A very large number of soybean accessions are stored in gene banks, but less than 1% of them have been used for breeding. Here, we present genotypic data as well as phenotypic data on plant and seed performance, including seed chlorophyll fluorescence traits, and on yield components within a collection of soybean accessions that are conserved in the Polish Gene Bank at the Plant Breeding and Acclimatization Institute-National Research Institute. Results The materials used consisted of sub-collections: 79 Polish genotypes, including old traditional cultivars, 24 Canadian, 21 American, 21 Swedish and 31 from Central and Eastern European Countries, 9 from France and 6 from Japan. In total, 9602 high quality SNPs were derived from DArTseq, a method utilising GBS technology. GWAS, performed with the BLINK model, revealed that a total of 41 significant SNPs were mapped for days to flowering, flower colour, plant height, days to pod formation, 100 seed weight, pod colour, seeds and hilum colour and steady-state chlorophyll fluorescence under light (Ft_Lss). This is the first report about the diversity of traditional old Polish soybean cultivars.

Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb

Background and Aims: Quantifying genetic variation is fundamental to understand a species’ demographic trajectory and its ability to adapt to future changes. In comparison with diploids, however, genetic variation and factors fostering genetic divergence remain poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies.Methods: We collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing. In addition, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high-quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations, complemented by genome size measurements and chromosomal counts. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables.Key Results: We found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modeling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria.Conclusion: Current findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.

De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.