Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper(Plectropomus leopardus)

The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.

Utilizing resequencing big data to facilitate Brassica vegetable breeding:tracing introgression pedigree and developing highly specific markers for clubroot resistance

Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable species B.rapa and B.oleracea,several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding.However,the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders'most urgent concerns.The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs.Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data.In B.rapa,a major locus CRzi8 underlying the CR of the commercial CR donor‘DegaoCR117’was identified.CRzi8 was further shown to have been introgressed from turnip(B.rapa ssp.rapifera)and that it carried a potential functional allele of Crr1a.The turnip introgression carried CRb^(c),sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B.oleracea CR cultivars with different morphotypes.Within natural populations,variation analysis of linkage intervals of CRzi8,PbBa8.1,CRb,and CRb^(c)yielded easily resolved InDel markers(>20 bp)for these fundamental CR genes.The specificity of these markers was tested in diverse cultivars panels,and each exhibited high reliability in breeding.Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs.

QTL mapping for berry shape based on a high-density genetic map constructed by whole-genome resequencing in grape

Grape berry shape is an important agricultural trait.Clarifying its genetic basis is significant for cultivating grape varieties that meet market demands.However,the current study by forward genetics has not achieved in-depth results.Here,a high-density map was constructed to identify quantitative trait loci(QTLs)for berry shape.A total of 358709 polymorphic SNPs were obtained using whole-genome resequencing(WGS)based on 208 F2 individuals derived from round grape‘E42-6’and oblong grape‘Rizamat’.The 1635.65 cM high-density map was divided into 19 linkage groups with an average distance of 0.37 cM.Using this map,three significant QTLs for fruit shape index(ShI:ratio of berry length to berry width)identified over three years were mapped onto LG4 and LG5,including one stable QTL on Chr5 with the genomic region of 0.47–1.94 Mb.Combining with gene annotation and expression patterns based on RNA-seq data from two contrasting F2 individuals with round and oblong berry(their average ShI was 1.89 and 1.10,respectively)at four developmental stages,four candidate genes were selected from the above QTLs.They were mainly involved in DNA replication,cell wall modification,and phytohormone biosynthesis.Further analysis of RNA-seq data revealed that several important phytohormone synthesis and metabolic pathways were enriched based on differentially expressed genes(DEGs),which was consistent with the results of QTL mapping for genes related to plant hormone biosynthesis in the F2 population.Furthermore,a comparison of plant hormone content showed that there were significant differences in IAA and tZ content between the two contrasting F2 individuals at different developmental stages.Our findings provide molecular insights into the genetic variation in grape berry shape.Stable QTLs and their tightly linked markers offer the possibility of marker-assisted selection to accelerate berry shape breeding.

Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass(Micropterus salmoides)

Largemouth bass(Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study,we sequenced 149 largemouth bass fish, including protospecies(imported from the US) and improved breeds(four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection,including several associated with growth(psst1 and grb10), early development(klf9, sp4, and sp8), and immune traits(pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.

QTL mapping of quality traits in peanut using whole-genome resequencing

Oil and protein content and fatty acid composition are quality traits in peanut.Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars by molecular breeding.Whole-genome resequencing of a recombinant inbred population of 318 lines was performed to construct a high-density linkage map and identify QTL for peanut quality.The map,containing 4561 bin markers,covered 2032 c M with a mean marker density of 0.45 c M.A total of 110 QTL for oil and protein content,and fatty acid composition were mapped on the 18 peanut chromosomes.The QTL q A05.1 was detected in four environments and showed a major phenotypic effect on the contents of oil,protein,and six fatty acids.The genomic region spanned by q A05.1,corresponding to a physical interval of approximately 1.5 Mb,contains two SNPs polymorphic between the parents that could cause missense mutations.The two SNP sites were employed as KASP markers and validated using lines with extremely high and low oil contents.These sites may be useful in the marker-assisted breeding of peanut cultivars with high oil contents.

Whole-genome resequencing of Japanese whiting(Sillago japonica) provide insights into local adaptations

The genetic adaptations of various organisms to heterogeneous environments in the northwestern Pacific remain poorly understood.Heterogeneous genomic divergence among populations may reflect environmentalselection.Advancingour understanding of the mechanisms by which organisms adapt to different temperatures in response to climate change and predicting the adaptive potential and ecological consequences of anthropogenic global warming are critical.We sequenced the whole genomes of Japanese whiting(Sillago japonica)specimens collected from different latitudinal locations along the coastal waters of China and Japan to detect possible thermal adaptations.Using population genomics,a total of 5.48 million single nucleotide polymorphisms(SNPs)from five populations revealed a complete genetic break between the Chinese and Japanese groups,which was attributed to both geographic distance and local adaptation.The shared natural selection genes between two isolated populations(i.e.,Zhoushan and Ise Bay/Tokyo Bay)indicated possible parallel evolution at the genetic level induced by temperature.These genes also indicated that the process of temperature selection on isolated populations is repeatable.Moreover,we observed natural candidate genes related to membrane fluidity,possibly underlying adaptation to cold environmental stress.These findings advance our understanding of the genetic mechanisms underlying the rapid adaptations of fish species.Species distribution projection models suggested that the Chinese and Japanese groups may have different responses to future climate change,with the former expanding and the latter contracting.The findings of this study enhance our understanding of genetic differentiation and adaptation to changing environments.

Whole-genome resequencing reveals molecular imprints of anthropogenic and natural selection in wild and domesticated sheep

The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying phenotypic variation induced by the domestication and improvement of sheep. In this study, to explore genomic diversity and selective regions at the genome level, we sequenced the genomes of 100 sheep across 10 breeds and combined these results with publicly available genomic data from 225 individuals, including improved breeds, Chinese indigenous breeds,African indigenous breeds, and their Asian mouflon ancestor. Based on population structure, the domesticated sheep formed a monophyletic group,while the Chinese indigenous sheep showed a clear geographical distribution trend. Comparative genomic analysis of domestication identified several selective signatures, including IFI44 and IFI44L genes and PANK2 and RNF24 genes, associated with immune response and visual function.Population genomic analysis of improvement demonstrated that candidate genes of selected regions were mainly associated with pigmentation,energy metabolism, and growth development.Furthermore, the IFI44 and IFI44L genes showed a common selection signature in the genomes of 30domesticated sheep breeds. The IFI44 c. 54413058C>G mutation was selected for genotyping and population genetic validation. Results showed that the IFI44 polymorphism was significantly associated with partial immune traits. Our findings identified the population genetic basis of domesticated sheep at the whole-genome level, providing theoretical insights into the molecular mechanism underlying breed characteristics and phenotypic changes during sheep domestication and improvement.

Refinement of four major QTL for oil content in Brassica napus by integration of genome resequencing and transcriptomics

Rapeseed(Brassica napus)supplies about half of the vegetable oil in China.Increasing oil production and searching for genes that control oil content in the crop are research goals.In our previous studies,four major QTL for oil content located on A08,A09,C03 and C06 in the Ken C-8×N53-2(KN DH)mapping population were detected.The parental lines were resequenced to identify structural variations and candidate genes affecting oil content in these four major QTL regions.Insertion-deletion(In Del)markers were developed and used to narrow the regions.Differentially expressed genes located in the regions were investigated.GO and KEGG analysis showed that several genes were associated with lipid metabolism.Several transcription factors with higher expression in N53-2 than in Ken C-8 were identified.These results shed light on the genetic control of oil content and may be helpful for the development of highoil-content cultivars.

Identification of Nucleus Sterility Candidate Genes Using a Resequencing Technique in Sweet Pepper Sterile Line AB91

Breeding hybrids with nuclear malesterile lines is an important method for the cross-breeding of sweet peppers. To date, few reports have been published on the nuclear malesterility gene of sweet pepper. Yet, there are approximately 20 pepper nuclear malesterility lines in the world. Using the self-developed testing material, sweet pepper nuclear malesterile dual-purpose line AB91, the genome-wide resequencing technique was applied to find that the mutation site causing the abortion of sweet pepper nuclear malesterility AB91 is on chromosome #5. The mutation gene Capana05g000747 was filtered out and validated by the flight mass spectrometry genotyping and quantitative realtime PCR method and determined to be the gene causing the abortion of sweet pepper nuclear male sterility AB91. The gene Capana05g000747 mutation site is a non-synonymous mutation site located at the 6th exon, the base C mutated into A, and the amino acid changed from alanine to serine. The three-dimensional protein structure of fertile and sterile plant Capana05g000747 was predicted. The results showed that the three-dimensional structure of the two proteins differed significantly. Sequence alignment analysis showed that the gene Capana05g000747 has a similar function to gene At2g02148. The gene At2g02148 contains a pentatricopeptide repeat protein which has important physiological functions in the gene expression process of organelles and is closely related to the performance of malesterility genes. Therefore, Capana05g000747 was selected as an important candidate gene for sweet pepper nuclear male sterile testing material AB91.

Identifying candidate genes involved in trichome formation on carrot stems by transcriptome profiling and resequencing

Trichomes are specialized structures developed from epidermal cells and can protect plants against biotic and abiotic stresses.Trichomes cover carrots during the generative phase.However,the morphology of the carrot trichomes and candidate genes controlling the formation of trichomes are still unclear.This study found that carrot trichomes were nonglandular and unbranched hairs distributed on the stem,leaf,petiole,pedicel,and seed of carrot.Resequencing analysis of a trichome mutant with sparse and short trichomes(sst)and a wild type(wt)with long and dense trichomes on carrot stems was conducted.A total of 15396 genes containing nonsynonymous mutations in sst were obtained,including 42 trichomerelated genes.We also analyzed the transcriptome of the trichomes on secondary branches when these secondary branches were 10 cm long between wt and sst and obtained 6576 differentially expressed genes(DEGs),including 24 trichome-related genes.qRT-PCR validation exhibited three significantly up-regulated DEGs,20 significantly downregulated,and one with no difference.We considered both the resequencing and transcriptome sequencing analyses and found that 12 trichome-related genes that were grouped into five transcription factor families containing nonsynonymous mutations and significantly down-regulated in sst.Therefore,these genes are potentially promising candidate genes whose nonsynonymous mutations and down-regulation may result in scarce and short trichomes mutation on carrot stems in sst.

Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits

The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human civilization.Hu sheep are a local sheep breed unique to China with high reproductive rates and rapid growth.Genomic selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in livestock.Here,we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep(Asiatic mouflon)to investigate the genetic characteristics and selection signatures of Hu sheep.Based on six signatures of selection approaches,we detect genomic regions containing genes related to reproduction(BMPR1B,BMP2,PGFS,CYP19,CAMK4,GGT5,and GNAQ),vision(ALDH1A2,SAG,and PDE6B),nervous system(NAV1),and immune response(GPR35,SH2B2,PIK3R3,and HRAS).Association analysis with a population of 1299 Hu sheep reveals that those missense mutations in the GPR35(GPR35 g.952651 A>G;GPR35 g.952496 C>T)and NAV1(NAV1 g.84216190 C>T;NAV1 g.84227412 G>A)genes are significantly associated(P<0.05)with immune and growth traits in Hu sheep,respectively.This research offers unique insights into the selection characteristics of Hu sheep and facilitates further genetic improvement and molecular investigations.

Plant genome resequencing and population genomics:Current status and future prospects

Advances in DNA sequencing technology have sparked a genomics revolution,driving breakthroughs in plant genetics and crop breeding.Recently,the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement.This transformation has been facilitated by the increasing adoption of whole-genome resequencing.In this review,we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding.A total of 187 land plants from 163 countries have been resequenced,comprising 54413 accessions.As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted.Economically important crops,particularly cereals,vegetables,and legumes,have dominated the resequencing efforts,leaving a gap in 49 orders,including Lycopodiales,Liliales,Acorales,Austrobaileyales,and Commelinales.The resequenced germplasm is distributed across diverse geographic locations,providing a global perspective on plant genomics.We highlight genes that have been selected during domestication,or associated with agronomic traits,and form a repository of candidate genes for future research and application.Despite the opportunities for cross-species comparative genomics,many population genomic datasets are not accessible,impeding secondary analyses.We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy.The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs,coupled with advances in analysis and computational technologies.This expansion,in terms of both scale and quality,holds promise for deeper insights into plant trait genetics and breeding design.

Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence

Rapeseed (Brassica napus),an important oilseed crop,has adapted to diverse climate zones and latitudes by forming three main ecotype groups,namely winter,semiwinter,and spring types. However,genetic variations underlying the divergence of these ecotypes are largely unknown. Here,we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions.A total of 5.56 and 5.53 million singlenucleotide polymorphisms (SNPs)as Well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of "Darmor-bzh"and "Tapidor,"respectively.We generated a map of allelic drift paths that shows splits and mixtures of the main populations,and revealed an asymmetric evolution of the two subgenomes of B.napus by calculating the genetic diversity and linkage disequilibrium parameters.Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses.A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups,and will facilitate screening of molecular markers for accelerating rapeseed breeding.

Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation

Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat.Uncovering the landscape of genetic variations in T.urartu will help us understand the evolutionary and polyploid characteristics of wheat.Here,we investigated the population genomics of T.urartu by genome-wide sequencing of 59 representative accessions collected around the world.A total of 42.2 million highquality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome.The ancient T.urartu population experienced a significant reduction in effective population size(Ne)from3000000 to140000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period.A map of allelic drift paths displayed splits and mixtures between different geographic groups,and a strong genetic drift towards hexaploid wheat was also observed,indicating that the direct donor of the A subgenome originated from northwestern Syria.Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses.A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T.urartu ecotype groups.Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomicsenabled improvements in wheat breeding.

Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei(Rubus corchorifolius)

Rubus corchorifolius(Shanmei or mountain berry,2n=14)is widely distributed in China,and its fruits possess high nutritional and medicinal values.Here,we reported a highquality chromosome-scale genome assembly of Shanmei,with contig size of 215.69 Mb and 26,696 genes.Genome comparison among Rosaceae species showed that Shanmei and Fupenzi(Rubus chingii Hu)were most closely related,followed by blackberry(Rubus occidentalis),and that environmental adaptation-related genes were expanded in the Shanmei genome.Further resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan,Hunan,Jiangxi,and Sichuan in China revealed that among these samples,the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral population.Moreover,the Yunnan population underwent strong selection based on the nucleotide diversity,linkage disequilibrium,and historical effective population size analyses.Furthermore,genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways,indicating the genetic basis of adaptation of Shanmei to the local environment.The high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

Resequencing and genome-wide association studies of autotetraploid potato

Potato is the fourth most important food crop in the world.Although with a long history for breeding approaches,genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars,which limit the molecular breeding progression.By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center,with approximate 20-fold coverage,we revealed more than 27 million Single Nucleotide Polymorphisms and~3 million Insertion and Deletions with high quality and accuracy.Domestication analysis and genome-wide association studies(GWAS)identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance,providing informative insights into the selection and domestication of cultivar potato.In addition,GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals,especially those related to tuber size,small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis.Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.

Whole-genome sequencing study to identify candidate markers indicating susceptibility to type 2 diabetes in Bama miniature pigs

Background:Hundreds of single-nucleotide polymorphism(SNP)sites have been found to be potential genetic markers of type 2 diabetes mellitus(T2DM).However,SNPs related to T2DM in minipigs have been less reported.This study aimed to screen the T2DM-susceptible candidate SNP loci in Bama minipigs so as to improve the success rate of the minipig T2DM model.Methods:The genomic DNAs of three Bama minipigs with T2DM,six sibling lowsusceptibility minipigs with T2DM,and three normal control minipigs were compared by whole-genome sequencing.The T2DM Bama minipig-specific loci were obtained,and their functions were annotated.Meanwhile,the Biomart software was used to perform homology alignment with T2DM-related loci obtained from the human genome-wide association study to screen candidate SNP markers for T2DM in Bama miniature pigs.Results:Whole-genome resequencing detected 6960 specific loci in the minipigs with T2DM,and 13 loci corresponding to 9 diabetes-related genes were selected.Further,a set of 122 specific loci in 69 orthologous genes of human T2DM candidate genes were obtained in the pigs.Collectively,a batch of T2DM-susceptible candidate SNP markers in Bama minipigs,covering 16 genes and 135 loci,was established.Conclusions:Whole-genome sequencing and comparative genomics analysis of the orthologous genes in pigs that corresponded to the human T2DM-related variant loci successfully screened out T2DM-susceptible candidate markers in Bama miniature pigs.Using these loci to predict the susceptibility of the pigs before constructing an animal model of T2DM may help to establish an ideal animal model.

Genome-wide profiling of RNA editing sites in sheep

Background: The widely observed RNA-DNA differences(RDDs) have been found to be due to nucleotide alteration by RNA editing. Canonical RNA editing(i.e., A-to-I and C-to-U editing) mediated by the adenosine deaminases acting on RNA(ADAR) family and apolipoprotein B mRNA editing catalytic polypeptide-like(APOBEC)family during the transcriptional process is considered common and essential for the development of an individual.To date, an increasing number of RNA editing sites have been reported in human, rodents, and some farm animals;however, genome-wide detection of RNA editing events in sheep has not been reported. The aim of this study was to identify RNA editing events in sheep by comparing the RNA-seq and DNA-seq data from three biological replicates of the kidney and spleen tissues.Results: A total of 607 and 994 common edited sites within the three biological replicates were identified in the ovine kidney and spleen, respectively. Many of the RDDs were specific to an individual. The RNA editing-related genes identified in the present study might be evolved for specific biological functions in sheep, such as structural constituent of the cytoskeleton and microtubule-based processes. Furthermore, the edited sites found in the ovine BLCAP and NEIL1 genes are in line with those in previous reports on the porcine and human homologs, suggesting the existence of evolutionarily conserved RNA editing sites and they may play an important role in the structure and function of genes.Conclusions: Our study is the first to investigate RNA editing events in sheep. We screened out 607 and 994 RNA editing sites in three biological replicates of the ovine kidney and spleen and annotated 164 and 247 genes in the kidney and spleen, respectively. The gene function and conservation analysis of these RNA editing-related genes suggest that RNA editing is associated with important gene function in sheep. The putative functionally important RNA editing sites reported in the present study will help future studies on the relationship between these edited sites and the genetic traits in sheep.

Development and validation of InDel markers for identification of QTL underlying flowering time in soybean

Soybean [Glycine max(L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding for many useful agronomic traits. Next-generation sequence data available in public databases provides valuable information and offers new insights for rapid and efficient development of molecular markers. In this study, we attempted to show the feasibility and facility of using genomic resequencing data as raw material for identifying putative In Del markers. First, we identified 17,613 In Del sites among 56 soybean accessions and obtained 12,619 primer pairs. Second, we constructed a genetic map with a random subset of 2841 primer pairs and aligned 300 polymorphic markers with the 20 consensus linkage groups(LG). The total genetic distance was 2347.3 c M and the number of mapped markers per LG ranged from 10 to 23 with an average of 15 markers. The largest and smallest genetic distances between adjacent markers were 52.3 c M and 0.1 cM, respectively. Finally, we validated the genetic map constructed by newly developed In Del markers by QTL analysis of days to flowering(DTF) under different environments. One major QTL(qDTF4) and four minor QTL(qDTF20, qDTF13, qDTF12,and q DTF11) on 5 LGs were detected. These results demonstrate the utility of the In Del markers developed in this work for map-based cloning and molecular breeding in soybean.

Large-Scale Screening of Growth-Related Variants in Chinese Tongue Sole(Cynoglossus semilaevis)

Growth is the most valuable economic trait for improving aquaculture fish species,since fast growth can reduce labor cost and make more economic benefits.However,the knowledge about how many and which genes are related to the growth of Chi-nese tongue sole is limited.High-throughput sequencing screening of variants is a fast,economical and accurate assay to identify genes related to growth in crops,livestock and other aquaculture products.In the present study,genome-wide resequencing of 30 female Chinese tongue sole individuals from large and small groups to screen growth trait-related variations(SNPs,InDels)was carried out.In total,6545735 SNPs and 1016745 InDels were detected,while 31 genes related to growth traits were identified.Their functions were mainly involved in muscle architecture,post-embryonic development,neurosensory development and hormone regulation.Fur-thermore,18 of the 31 genes related to growth trait are located on W chromosome,indicating that W chromosome plays an important role in regulating the body size of female tongue soles.The markers and genes identified in our study can be applied to selective breeding of tongue sole and thus will promote the aquaculture industry and increase economic efficiency.