Analysis Of Genetic Population Structure Research Articles

Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus

BackgroundApostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. japonicus, mainly harvested in the Vladivostok region, exhibits significant phenotypic differentiation, including in many economically important traits, compared with Chinese A. japonicus owing to differences in their habitat. However, both the genetic basis for the phenotypic divergence and the population genetic structure of Russian and Chinese A. japonicus are unknown.ResultIn this study, 210 individuals from seven Russian and Chinese A. japonicus populations were sampled for whole-genome resequencing. The genetic structure analysis differentiated the Russian and Chinese A. japonicus into two groups. Population genetic analyses indicated that the Russian population showed a high degree of allelic linkage and had undergone stronger positive selection compared with the Chinese populations. Gene ontology terms enriched among candidate genes with group selection analysis were mainly involved in immunity, such as inflammatory response, antimicrobial peptides, humoral immunity, and apoptosis. Genome-wide association analysis yielded eight single-nucleotide polymorphism loci significantly associated with parapodium number, and these loci are located in regions with a high degree of genomic differentiation between the Chinese and Russia populations. These SNPs were associated with five genes. Gene expression validation revealed that three of these genes were significantly differentially expressed in individuals differing in parapodium number. AJAP08772 and AJAP08773 may directly affect parapodium production by promoting endothelial cell proliferation and metabolism, whereas AJAP07248 indirectly affects parapodium production by participating in immune responses.ConclusionsThis study, we performed population genetic structure and GWAS analysis on Chinese and Russian A. japonicus, and found three candidate genes related to the number of parapodium. The results provide an in-depth understanding of the differences in the genetic structure of A. japonicus populations in China and Russia, and provide important information for subsequent genetic analysis and breeding of this species.

Phylogeographic analysis of the Japanese wild boar (<I>Sus scrofa leucomystax</I>)

The Japanese wild boar (Sus scrofa leucomystax) is an indigenous subspecies of the wild boar, which is distributed in Honshu, Shikoku, Kyushu, and other smaller islands of Japan. The distribution area of the Japanese wild boar has in the last 40 years expanded by 1.9-fold due to improved suitable survival conditions, such as global warming which has decreased snowfall, increased abandoned farmland, and decreased hunting pressure. As a result, the negative impacts of this population increase on humans continue to spread. In this study, 1,251 Japanese wild boars were sampled from 32 prefectures which nearly cover the entire expanded distribution area in Japan, and phylogeographical analysis was performed using 30 Measurement of Domestic Animal Diversity recommended microsatellite markers. Both neighbor-joining (NJ) phylogenetic trees constructed using Nei's DA genetic distance matrix and population genetic structure analysis classified Japanese wild boar into six phylogeographical subpopulations, including northern Honshu, eastern Honshu, central Honshu, western Honshu, Shikoku, and Kyushu. The six identified genetic subpopulations were speculated to form as a result of several factors, including human activity between the northern and eastern Honshu, occurrence of three mountain ranges of 3,000-meter height between the eastern and central Honshu, the inland sea between western Honshu and Shikoku, and the presence of strait between western Honshu and Kyushu. Interestingly, some individual wild boars from Gunma, Tochigi, and Miyazaki areas formed distinct and separate subpopulations, with animals within these subgroups exhibiting traits such as low genetic differentiation and high diversity, which likely suggested gene influx from domestic pigs or other sources.

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China.

The Qinghai Province of China is located in the northeast region of the Qinghai-Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data. We observed that most of Qinghai yak breeds/populations have abundant genomic diversity based on four genomic parameters (nucleotide diversity, inbreeding coefficients, linkage disequilibrium decay, and runs of homozygosity). Population genetic structure analysis showed that Qinghai yak have two lineages with two ancestral origins and that nine yak breeds/populations are clustered into three distinct groups of wild yak, Geermu yak, and seven other domestic yak breeds/populations. F ST values showed moderate genetic differentiation between wild yak, Geermu yak, and the other Qinghai yak breeds/populations. Positive selection signals were detected in candidate genes associated with disease resistance (CDK2AP2, PLEC, and CYB5B), heat stress (NFAT5, HSF1, and SLC25A48), pigmentation (MCAM, RNF26, and BOP1), vision (C1QTNF5, MFRP, and TAX1BP3), milk quality (OPLAH and GRINA), neurodevelopment (SUSD4, INSYN1, and PPP1CA), and meat quality (ZRANB1), using the integrated PI, composite likelihood ratio (CLR), and F ST methods. These findings offer new insights into the genetic mechanisms underlying target traits in yak and provide important information for understanding the genomic characteristics of yak breeds/populations in Qinghai.

Genetic Signature of Pinctada fucata Inferred from Population Genomics: Source Tracking of the Invasion in Mischief Reef of Nansha Islands.

Among the anthropogenic stresses that marine ecosystems face, biological invasions are one of the major threats. Recently, as a result of increasingly intense anthropogenic disturbance, numerous marine species have been introduced to their non-native ranges. However, many introduced species have uncertain original sources. This prevents the design and establishment of methods for controlling or preventing these introduced species. In the present study, genomic sequencing and population genetic analysis were performed to detect the geographic origin of the introduced Pinctada fucata population in the Mischief Reef of the South China Sea. The results of population genetic structure analysis showed a close relationship between the Mischief Reef introduced population and the Lingshui population, indicating that Lingshui may be the potential geographical origin. Furthermore, lower heterozygosity and nucleotide diversity were observed in the introduced population in Mischief Reef, indicating lower genetic diversity than in other native populations. We also identified some selected genomic regions and genes of the introduced population, including genes related to temperature and salinity tolerance. These genes may play important roles in the adaptation of the introduced population. Our study will improve our understanding of the invasion history of the P. fucata population. Furthermore, the results of the present study will also facilitate further control and prevention of invasion in Mischief Reef, South China Sea.

Genetic diversity and breed identification of Chinese and Vietnamese local chicken breeds based on microsatellite analysis.

South Asia and Southeast Asia are the origins of domestic chickens and are rich in poultry genetic resources, resulting in many unique local chicken breeds. However, with the rapid intensification of poultry farming worldwide, many local chicken breeds are threatened with extinction. In response to China's "One Belt, One Road" policy, it is imperative to strengthen the conservation and breeding of local chicken breeds in China and Vietnam. This study characterized 18 microsatellite molecular genetic markers to analyze the genetic diversity of 21 local chicken populations in southern China (Yunnan and Guangxi Provinces) and Vietnam, breed identification tags for microsatellite loci were constructed. The results showed that a total of 377 alleles were detected in all breeds, and the most alleles (44) and the highest polymorphic information content (0.7820) were detected at the LEI0094 locus. The average polymorphic information content (PIC) content of the whole population was 0.65, indicating moderate polymorphism. The genetic diversity of the whole population was rich, except for two loci MCW0111 and MCW0016, that showed heterozygote excess at microsatellite loci, and the population had high genetic differentiation. The Vietnamese breeds showed low pairwise fixation coefficient (FST) and Nei's standard genetic distance (DS) between them. According to the neighbor-joining dendrogram constructed by DS and the analysis of population genetic structure using the structure program, Longshengfeng chicken, Yunlong dwarf chicken, Tengchong white chicken, Xiayan chicken, and Daweishan mini chicken are similar, and Xishuangbanna game fowl, Wuding chicken, and Lanping silky chicken are similar to Yanjin black-bone chicken. In addition, excluding Dongtao chicken, other Vietnamese breeds are clustered together, indicating that the southern chicken breeds are closely related and have experienced better breeding. Overall, the whole population is rich in genetic resources, and the chicken breeds in the three regions are genetically close because of geographical factors and human activities. Dongtao chicken in Vietnamese, Chinese Yunnan local chicken breeds (Gallus gallus spadiceus), and red jungle fowl chickens (Gallus gallus) may have the same origin. We also constructed unique microsatellite molecular markers for 20 cultivars using 15 microsatellite loci. This study provides valuable insights to facilitate breed identification, improve cultivar protection, and new germplasm construction.

Evolution of a hybrid zone of two willow species (Salix L.) in the European Alps analyzed by RAD-seq and morphometrics.

Natural hybridization of plants can result in many outcomes with several evolutionary consequences, such as hybrid speciation and introgression. Natural hybrid zones can arise in mountain systems as a result of fluctuating climate during the exchange of glacial and interglacial periods, where species retract and expand their territories, resulting in secondary contacts. Willows are a large genus of woody plants with an immense capability of interspecific crossing. In this study, the sympatric area of two diploid sister species, S.foetida and S.waldsteiniana in the eastern European Alps, was investigated to study the genomic structure of populations within and outside their contact zone and to analyze congruence of morphological phenotypes with genetic data. Eleven populations of the two species were sampled across the Alps and examined using phylogenetic network and population genetic structure analyses of RAD Seq data and morphometric analyses of leaves. The results showed that a homoploid hybrid zone between the two species was established within their sympatric area. Patterns of genetic admixture in homoploid hybrids indicated introgression with asymmetric backcrossing to not only one of the parental species but also one hybrid population forming a separate lineage. The lack of F1 hybrids indicated a long-term persistence of the hybrid populations. Insignificant isolation by distance suggests that gene flow can act over large geographical scales. Morphometric characteristics of hybrids supported the molecular data and clearly separated populations of the parental species, but showed intermediacy in the hybrid zone populations with a bias toward S.waldsteiniana. The homoploid hybrid zone might have been established via secondary contact hybridization, and its establishment was fostered by the low genetic divergence of parental species and a lack of strong intrinsic crossing barriers. Incomplete ecological separation and the ability of long-distance dispersal of willows could have contributed to the spatial expansion of the hybrid zone.

Pronounced Mitochondrial DNA Population Genetic Structure in a Brooding Coastal Marine Invertebrate

Analyses of phylogeographic and population genetic structure of marine species with large population sizes, low fecundity, larval brooding, and limited dispersal such as the New Zealand flat oyster, Ostrea chilensis Küster, 1844, permit testing of the effects of historical and contemporary processes affecting patterns of coastal genetic differentiation and diversity. Analyses of DNA sequences from two mitochondrial DNA regions (COI, Cyt-b) compiled from O. chilensis individuals from 14 localities revealed a pronounced structure with three genetic clusters [Hauraki Gulf (HG); North; South] being resolved. These results suggest that historical processes have contributed to patterns of regional separation that have in turn contributed to regional genetic differences that are still observable today. Divergence time estimates of HG from North+South (1.97 Ma) and of North from South (0.36 Ma) indicate that O. chilensis from these regions represent evolutionarily significant units that evolved separately and rapidly in the early to middle Pleistocene. Analyses revealed no obvious periods of population expansion within any of the regions. These results contribute to a better understanding of how historical factors can result in pronounced mitochondrial DNA patterns of contemporary genetic structure and show how key life-history characteristics, e.g., larval brooding, can contribute to phylogeographic structure in coastal marine invertebrates.

EST-SSR Markers' Development Based on RNA-Sequencing and Their Application in Population Genetic Structure and Diversity Analysis of Eleusine indica in China.

Goosegrass (Eleusine indica) is one of the worst agricultural weeds in China. Molecular markers were developed for genetic diversity and population structure analyses. In this study, we identified 8391 expressed sequence tag-simple sequence repeat (EST-SSR) markers from the de novo assembled unigenes of E. indica. Mononucleotides were the most abundant type of repeats (3591, 42.79%), followed by trinucleotides (3162, 37.68%). The most dominant mononucleotide and trinucleotide repeat motifs were A/T (3406, 40.59%) and AAT/ATT (103, 1.5%), respectively. Fourteen pairs of EST-SSR primers were verified and used to analyze the genetic diversity and population structure of 59 goosegrass populations. A total of 49 alleles were amplified, with the number of alleles (Na) ranging from two to eleven per locus, and the effective number of alleles (Ne) ranged from 1.07 to 4.53. The average polymorphic information content (PIC) was 0.36. Genetic structure analysis (K = 2) and principal coordinate analysis divided 59 E. indica populations into two groups in a manner similar to the unweighted pair-group method (Dice genetic similarity coefficient = 0.700). This study developed a set of EST-SSR markers in E. indica and successfully analyzed the diversity and population genetic structures of 59 E. indica populations in China.

Analysis of Genetic Polymorphism and Population Genetic Structure of 57 Autosomal InDel Loci in Beichuan Qiang Population.

To investigate the genetic information of 57 autosomal InDel loci (A-InDels) included in AGCU InDel 60 fluorescence detection kit in the Beichuan Qiang population of Sichuan Province and evaluate its application value in forensic medicine. A total of 200 unrelated healthy individuals from Beichuan Qiang population of Sichuan Province were typing detected by AGCU InDel 60 fluorescence detection kit. Allele frequencies and population genetic parameters of the 57 A-InDels were statistically analyzed and compared with the available data of 26 populations. After Bonferroni correction, there was no linkage disequilibrium between the 57 A-InDels, and all loci were in Hardy-Weinberg equilibrium. Except for rs66595817 and rs72085595, the minor allele frequencies of 55 A-InDels were above 0.3. PIC ranged from 0.298 3 to 0.375 0, CDP was 1-2.974 8×10-24, CPEduo was 0.999 062 660, and CPEtrio was 0.999 999 999. The calculation of the genetic distance showed that Beichuan Qiang population had the closest genetic distances with Beijing Han and South China Han populations, but far away from African populations. The 57 A-InDels in AGCU InDel 60 fluorescence detection kit have a good genetic polymorphism in Beichuan Qiang population of Sichuan Province, which can be used as effective supplemental for individual identification and paternity identification in forensic medicine.

Genetic diversity and spatial structure of indigenous sheep population of Benin revealed by microsatellite markers

This study investigated the genetic variability existing within the indigenous sheep population of Benin. Hair samples from 681 unrelated sheep collected across the 10 phytogeographic zones of Benin were genotyped using a set of 12 microsatellite markers. Genetic diversity indices, Bayesian ancestral admixture model, Self-Organizing Map (SOM), and Discriminant Analysis of Principal Components (DAPC), were performed to assess both the genetic diversity and spatial structure of the population under study. The polymorphism information content (PIC) recorded for each microsatellite marker used was greater than 0.50 with an average value of 0.70. The average number of alleles (12.17) and heterozygosity values (He = 0.73; Ho = 0.68) obtained suggest high genetic diversity within the Beninese sheep population. The population genetic structure analysis revealed two ancestral sheep populations in Benin, namely, the Djallonké and Sahelian sheep. Furthermore, SOM and DAPC identified four clusters of sheep within the 10 phytogeographic zones, including two Djallonké and two Sahelian subpopulations with some admixture. Djallonké sheep were predominant in the humid zones of southern Benin, with one subpopulation mainly present in the Pobè and Oueme Valley zones, and the second in Coastal, Plateau, and Zou zones. The latter subpopulation seemed the most admixed, with a mean Djallonké ancestral proportion of 86.15%. Sahelian sheep were predominant in the phytogeographic zones of northern Benin. Sheep from the driest North zone consisted the first Sahelian subpopulation and had a higher Sahelian ancestry proportion (89.81%) compared to the second subpopulation (69.29%) that most consisted of sheep from the other phytogeographic zones of the North.

Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs.

Yunan is a crossed lean meat pig breed in China. Backfat thickness is the gold standard for carcass quality grading. However, over 14years after breed registration, the backfat of Yunan thickened and the consistency of backfat thickness decreased. Meanwhile, no genetic study has been ever performed on Yunan population. So, in this study we collected all the 120 nucleus individuals of Yunan and recorded six backfat traits of them, carried out population genetic structure analysis, selection signals analysis and genome-wide association study of Yunan pigs with the help of their founder population Duroc and Chinese native Huainan pigs, to determine the genomic loci on backfat of Yunan. Genetic diversity indexes suggested Yunan pigs had no inbreeding risk while population genetic structure showed they had few molecular pedigrees and were stratified. A total of 71 common selection signals affecting growth and fat deposition were detected by F ST and XP-CLR methods. 34 significant loci associated with six backfat traits were detected, among which a 1.40Mb region on SSC4 (20.03-21.43Mb) were outstanding as the strong region underlying backfat. This region was common with the results of selection signature analysis, former reported QTLs for backfat and was common for different kinds of backfat traits at different development stage. ENPP2, EXT1 and SLC30A8 genes around were fat deposition related genes and were of Huainan pig's origin, among which Type 2 diabetes related gene SLC30A8 was the most reasonable for being in a 193.21Kb haplotype block of the 1.40Mb region. Our results had application value for conservation, mating and breeding improvement of backfat thickness of Yunan pigs and provided evidence for a human function gene might be reproduced in pigs.

Association mapping for important agronomic traits in wild and cultivated Vigna species using cross-species and cross-genera simple sequence repeat markers.

The genus Vigna is an agronomically important taxon, with many of its species inhabiting a wide range of environments and offering numerous useful genes for the improvement of the cultivated types. The present study aimed to detect the genomic regions associated with yield-attributing traits by genome-wide association mapping. A diverse panel of 98 wild and cultivated Vigna accessions (acc.) belonging to 13 different species was evaluated for yield and related traits during the kharif season of 2017 and 2018. The panel was also genotyped using 92 cross-genera and cross-species simple sequence repeat markers to study the population genetic structure and useful market-trait associations. The PCA and trait correlation established relationships amongst the traits during both seasons while 100-seed weight (HSW) had a positive correlation with pod length (PL), and days to first flowering (DFF) with days to maturity (DM). The population genetic structure analysis grouped different acc. into three genetically distinct sub-populations with SP-1 comprising 34 acc., SP-2 (24 acc.), and SP-3 (33 acc.) and one admixture group (7 acc.). Mixed linear model analysis revealed an association of 13 markers, namely, VR018, VR039, VR022, CEDG033, GMES0337, MBSSR008, CEDG220, VM27, CP1225, CP08695, CEDG100, CEDG008, and CEDG096A with nine traits. Seven of the aforementioned markers, namely, VR018 for plant height (PH) and terminal leaflet length (TLL), VR022 for HSW and pod length (PL), CEDG033 for DFF and DM, MBSSR008 for DFF and DM, CP1225 for CC at 30 days (CC30), DFF and DM, CEDG100 for PH and terminal leaflet length (TLL), and CEDG096A for CC30 and chlorophyll content at 45 days were associated with multiple traits. The marker CEDG100, associated with HSW, PH, and TLL, is co-localized in gene-encoding histone-lysine N-methyltransferase ATX5. Similarly, VR22, associated with PL and HSW, is co-located in gene-encoding SHOOT GRAVITROPISM 5 in mungbean. These associations may be highly useful for marker-assisted genetic improvement of mungbean and other related Vigna species.

Deploying Community Scientists to Conduct Nondestructive Genetic Sampling of Rare Butterfly Populations.

Global insect declines continue to accelerate. Effective genetic sampling is critically needed to advance the understanding of many taxa and address existing knowledge gaps. This protocol represents a demonstrated method for nondestructively sampling rare butterflies for population genetic structure or DNA barcoding analyses. It uses the chorion of hatched butterfly ovae to yield sufficiently high quantity and quality DNA for successful gene sequencing to confirm species identity and quantify genetic variation. It may be particularly useful when other tissue sampling techniques are impractical or unavailable. While developed for a lepidopteran, it nonetheless could easily be adapted for use with other insect species. It was specifically designed with ease of use as a goal to help maximize broad implementation by individuals of varying experience and skill levels, such as community scientists, conservation practitioners, and students, and for use over large geographic areas to facilitate broad population sampling. The data generated can help inform taxonomic and listing decisions, conservation and management actions, and enhance basic ecological research.

De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn.

BackgroundSagittaria trifolia Linn. is a widespread macrophyte in Asia and southeast Europe and cultivated in parts of Asia. Although a few genomic studies have been conducted for S. trifolia var. sinensis, a crop breed, there is limited genomic information on the wild species of S. trifolia. Effective microsatellite markers are also lacking.ObjectiveTo assemble transcriptome sequence and develop effective EST-SSR markers for S. trifolia.MethodsHere we developed microsatellite markers based on tri-, tetra-, penta-, and hexa-nucleotide repeat sequences by comparatively screening multiple transcriptome sequences of eleven individuals from ten natural populations of S. trifolia.ResultsA total of 107,022 unigenes were de novo assembled, with a mean length of 730 bp and an N50 length of 1,378 bp. The main repeat types were mononucleotide, trinucleotide, and dinucleotide, accounting for 55.83%, 23.51%, and 17.56% of the total repeats, respectively. A total of 86 microsatellite loci were identified with repeats of tri-, tetra-, penta-, and hexa-nucleotide. For SSR verification, 28 polymorphic loci from 41 randomly picked markers were found to produce stable and polymorphic bands, with the number of alleles per locus ranging from 2 to 11 and a mean of 5.2. The range of polymorphic information content (PIC) of each SSR locus varied from 0.25 to 0.80, with an average of 0.58. The expected heterozygosity ranged from 0.29 to 0.82, whereas the observed heterozygosity ranged from 0.25 to 0.90.ConclusionThe assembled transcriptome and annotated unigenes of S. trifolia provide a basis for future studies on gene functions, pathways, and molecular mechanisms associated with this species and other related. The newly developed EST-SSR markers could be effective in examining population genetic structure, differentiation, and parentage analyses in ecological and evolutionary studies of S. trifolia.

Whole-Genome Resequencing Highlights the Unique Characteristics of Kecai Yaks.

Simple SummaryKecai yaks are an important genetic resource in Gansu Province, China. These yaks, produced through the crossbreeding of Gannan yaks and wild yaks, exhibit excellent production performance and high fecundity. Despite these beneficial characteristics, the genetic characteristics, population structure, and other properties of Kecai yaks have not been effectively characterized to date. Accordingly, this study was developed to explore the genetic diversity and population structure of Kecai yaks through whole-genome resequencing. These analyses ultimately revealed the status of Kecai yaks as an independent group within the overall Chinese yak population.Kecai yaks are regarded as an important genetic resource in China owing to their high fecundity and flavorful meat. However, the genetic characteristics of Kecai yaks have not been effectively characterized to date, and the relationship between Kecai yaks and other yak breeds remains to be fully characterized. In this paper, the resequencing of the Kecai yak genome is performed leading to the identification of 11,491,383 high-quality single nucleotide polymorphisms (SNPs). Through principal component, phylogenetic, and population genetic structure analyses based on these SNPs, Kecai yaks were confirmed to represent an independent population of yaks within China. In this study, marker and functional enrichment analysis of genes related to positive selection in Kecai yak was carried out, and the results show that such selection in Kecai yaks is associated with the adaptation to alpine environments and the deposition of muscle fat. Overall, these results offer a theoretical foundation for the future utilization of Kecai yak genetic resources.

Large-Scale Heat-Tolerance Screening and Genetic Diversity of Pea (Pisum sativum L.) Germplasms.

Pea (Pisum sativum L.) is an important legume crop. However, the yield of pea is adversely affected by heat stress in China. In this study, heat-tolerant germplasms were screened and evaluated in the field under multi-conditions. The results showed that heat stress could significantly affect pea yield. On the basis of grain weight per plant, 257 heat-tolerant and 175 heat-sensitive accessions were obtained from the first year’s screening, and 26 extremely heat-tolerant and 19 extremely heat-sensitive accessions were finally obtained in this study. Based on SNaPshot technology, two sets of SNP markers, including 46 neutral and 20 heat-tolerance-related markers, were used to evaluate the genetic diversity and population genetic structure of the 432 pea accessions obtained from the first year’s screening. Genetic diversity analysis showed that the average polymorphic information content was lower using heat-tolerance-related markers than neutral markers because of the selective pressure under heat stress. In addition, population genetic structure analysis showed that neutral markers divided the 432 pea accessions into two subpopulations associated with sowing date type and geographical origin, while the heat-tolerance-related markers divided these germplasms into two subpopulations associated with heat tolerance and sowing date type. Overall, we present a comprehensive resource of heat-tolerant and heat-sensitive pea accessions through heat-tolerance screenings in multi-conditions, which could help genetic improvements of pea in the future.

Correlations among population genetic structure, geographic origin, growth rate, and fungicide resistance of Rhizoctonia solani AG 1-IA, the pathogen of rice sheath blight

Rhizoctonia solani AG1-IA is a necrotrophic fungus that causes rice sheath blight and results in severe yield and quality reductions in rice worldwide. Differences of genetic structure and fungicide sensitivity of the pathogen have significant effects on the severity and control effect of this disease in the field. To determine correlations among population genetic structure, geographic origin, growth rate, and fungicide resistance of the pathogen, 293 strains of R. solani were isolated from diseased rice collected from 13 cities of Jiangsu Province and five regions of China. Simple sequence repeat (SSR) molecular marker technology was used to analyze the genetic diversity of these strains, and a total of 74 bands were amplified by nine pairs of primers. Population genetic structure analysis showed that strains from Central China and northern Jiangsu had the highest Nei’s gene diversity index and Shannon diversity index. The vast majority of strains grew fast with colony diameters of more than 60.0 mm cultured at 28 °C for 36 h. The half-maximal effective concentration (EC50) of them to tebuconazole, thifluzamide, and propiconazole varied ∼16.2-, 3.8-, and 7.5-fold. However, the genetic diversity of R. solani had no significant correlation with their geographic origin, growth rate or fungicide sensitivity.

Analysis of waxy maize germplasm resources in Southwest China based on SNP markers

Waxy maize (Zea mays L. var. ceratina Kulesh) is an important economic crop in China, most of which are distributed in Southwestern China. In this study, 30 main waxy maize inbred lines in Southwest China were used as materials, and genetic analysis of the tested waxy corn materials was carried out using high-quality single nucleotide polymorphism (SNP) marker technology. A total of 15,111 SNPs were obtained from 30 test materials, and the genetic similarity coefficient varied from 0.4568 to 0.9974. The results of population genetic structure and principal component analysis showed that the tested waxy maize materials and the commonly used common maize classification representative inbred lines (B73, ZI330, Mo17, Huangzao 4, etc.) could not be effectively clustered. The 30 waxy corn materials can be divided into five groups separately. The application of the genetic relationship between materials identified by SNP analysis will enable breeders to select different parents to develop high-yield varieties with improved quality traits.

Analysis of Population Genetic Diversity and Genetic Structure of Schizothorax biddulphi Based on 20 Newly Developed SSR Markers

To protect the germplasm resources of Schizothorax biddulphi, we developed and used 20 pairs of polymorphic microsatellite primers to analyze the genetic diversity and structure of populations. A total of 126 samples were collected from the Qarqan River (CEC), Kizil River (KZL), and Aksu River (AKS) in Xinjiang, China. The results showed that 380 alleles were detected in 20 pairs of primers and the average number of alleles was 19.0. The effective allele numbers and Nei’s gene diversity ranged from 1.1499 to 1.1630 and 0.0962 to 0.1136, respectively. The Shannon index range suggested low levels of genetic diversity in all populations. The genetic distance between the CEC and AKS populations was the largest, and the genetic similarity was the smallest. There was a significant genetic differentiation between CEC and the other two populations. The UPGMA clustering tree was constructed based on population genetic distance, and the clustering tree constructed by individuals showed that the AKS population and KZL population were clustered together, and the CEC population was clustered separately. Also, the group structure analysis also got the same result. It can be seen that although the three populations of S. biddulphi do not have high genetic diversity, the differentiation between the populations was high and the gene flow was limited, especially the differentiation between the CEC population and the other two populations. This study not only provided genetic markers for the research of S. biddulphi but the results of this study also suggested the need for enhanced management of S. biddulphi populations.

Delimiting continuity: Comparison of target enrichment and double digest restriction‐site associated DNA sequencing for delineating admixing parapatric Melitaea butterflies

AbstractParapatrically distributed taxa pose a challenge for species delimitation due to the presence of gene flow and inherent arbitrariness of exactly defining the species boundaries in such systems. We tackled the problem of species delimitation in a parapatric species pair of Melitaea butterflies using two popular genomic methods—double digest restriction‐site associated DNA sequencing (ddRAD) and target enrichment. We compared newly generated target enrichment dataset with 1733 loci to the already available ddRAD data from a previous study on the same set of specimens using a suite of phylogenetic, population genetic, and species delimitation methods. We recovered consistent phylogenetic relationships across the datasets, both demonstrating the presence of a genetically distinct Balkan lineage and paraphyly of Melitaea athalia with respect to Melitaea celadussa. Population genetic STRUCTURE analyses supported the presence of two species when using ddRAD data, but three species when using target enrichment, while a Bayes factor delimitation analysis found both two and three species scenarios equally decisive in both datasets. As the results obtained from both methods were largely congruent, we discuss some practical considerations and benefits of target enrichment over RAD sequencing. We conclude that the choice of method of genomic data collection does not influence the results of phylogenetic analyses at alpha taxonomic level, given a sufficient number of loci. Finally, we recommend a solution for delineating species in parapatric scenarios by proposing that parapatric taxa be consistently classified as subspecies or complete species, but not both, to promote taxonomic stability.