Construction Of High-density Genetic Map Research Articles

High-density genetic map construction and QTL mapping of a zigzag-shaped stem trait in tea plant (Camellia sinensis)

The highly unique zigzag-shaped stem phenotype in tea plants boasts significant ornamental value and is exceptionally rare. To investigate the genetic mechanism behind this trait, we developed BC1 artificial hybrid populations. Our genetic analysis revealed the zigzag-shaped trait as a qualitative trait. Utilizing whole-genome resequencing, we constructed a high-density genetic map from the BC1 population, incorporating 5,250 SNP markers across 15 linkage groups, covering 3,328.51 cM with an average marker interval distance of 0.68 cM. A quantitative trait locus (QTL) for the zigzag-shaped trait was identified on chromosome 4, within a 61.2 to 97.2 Mb range, accounting for a phenotypic variation explained (PVE) value of 13.62%. Within this QTL, six candidate genes were pinpointed. To better understand their roles, we analyzed gene expression in various tissues and individuals with erect and zigzag-shaped stems. The results implicated CsXTH (CSS0035625) and CsCIPK14 (CSS0044366) as potential key contributors to the zigzag-shaped stem formation. These discoveries lay a robust foundation for future functional genetic mapping and tea plant genetic enhancement.

Construction of high-density genetic map based on SLAF-seq and QTL analysis of major traits in sweetpotato [Ipomoea batatas (L.) Lam.]

Sweetpotato, Ipomoea batatas (L.) Lam., is an important worldwide crop used as feed, food, and fuel. However, its polyploidy, high heterozygosity and self-incompatibility makes it difficult to study its genetics and genomics. Longest vine length (LVL), yield per plant (YPP), dry matter content (DMC), starch content (SC), soluble sugar content (SSC), and carotenoid content (CC) are some of the major agronomic traits being used to evaluate sweetpotato. However limited research has actually examined how these traits are inherited. Therefore, after selecting 212 F1 from a Xin24 × Yushu10 crossing as the mapping population, this study applied specific-locus amplified fragment sequencing (SLAF-seq), at an average sequencing depth of 26.73 × (parents) and 52.25 × (progeny), to detect single nucleotide polymorphisms (SNPs). This approach generated an integrated genetic map of length 2441.56 cM and a mean distance of 0.51 cM between adjacent markers, encompassing 15 linkage groups (LGs). Based on the linkage map, 26 quantitative trait loci (QTLs), comprising six QTLs for LVL, six QTLs for YPP, ten QTLs for DMC, one QTL for SC, one QTL for SSC, and two QTLs for CC, were identified. Each of these QTLs explained 6.3–10% of the phenotypic variation. It is expected that the findings will be of benefit for marker-assisted breeding and gene cloning of sweetpotato.

A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize (Zea mays L.).

The leaf scorching trait at flowering is a crucial thermosensitive phenotype in maize under high temperature stress (HS), yet the genetic basis of this trait remains poorly understood. In this study, we genotyped a 254 RIL-F2:8 population, derived from the leaf scorch-free parental inbred line Abe2 and the leaf scorching maternal inbred line B73, using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 10,112 polymorphic SLAF markers were developed, and a high-density genetic map with a total length of 1,475.88 cM was constructed. The average sequencing depth of the parents was 55.23X, and that of the progeny was 12.53X. Then, we identified a total of 16 QTLs associated with thermotolerant traits at flowering, of which four QTLs of leaf scorching damage (LS) were distributed on chromosomes 1 (qLS1), 2 (qLS2.1, qLS2.2) and 3 (qLS3), which could explain 19.73% of phenotypic variation. Combining one qLS1 locus with QTL-seq results led to the identification of 6 candidate genes. Expression experiments and sequence variation indicated that Zm00001d033328, encoding N-acetyl-gamma-glutamyl-phosphate reductase, was the most likely candidate gene controlling thermotolerant traits at flowering. In summary, the high-density genetic map and genetic basis of thermotolerant traits lay a critical foundation for mapping other complex traits and identifying the genes associated with thermotolerant traits in maize.

Construction of High-Density Genetic Map and QTL Mapping for Grain Shape in the Rice RIL Population.

Grain shape is an important agronomic trait directly associated with yield in rice. In order to explore new genes related to rice grain shape, a high-density genetic map containing 2193 Bin markers (526957 SNP) was constructed by whole-genome resequencing of 208 recombinant inbred (RILs) derived from a cross between ZP37 and R8605, with a total genetic distance of 1542.27 cM. The average genetic distance between markers was 0.76 cM, and the physical distance was 201.29 kb. Quantitative trait locus (QTL) mapping was performed for six agronomic traits related to rice grain length, grain width, length-to-width ratio, thousand-grain weight, grain cross-sectional area, and grain perimeter under three different environments. A total of 39 QTLs were identified, with mapping intervals ranging from 8.1 kb to 1781.6 kb and an average physical distance of 517.5 kb. Among them, 15 QTLs were repeatedly detected in multiple environments. Analysis of the genetic effects of the identified QTLs revealed 14 stable genetic loci, including three loci that overlapped with previously reported gene positions, and the remaining 11 loci were newly identified loci associated with two or more environments or traits. Locus 1, Locus 3, Locus 10, and Locus 14 were novel loci exhibiting pleiotropic effects on at least three traits and were detected in multiple environments. Locus 14, with a contribution rate greater than 10%, influenced grain width, length-to-width ratio, and grain cross-sectional area. Furthermore, pyramiding effects analysis of three stable genetic loci showed that increasing the number of QTL could effectively improve the phenotypic value of grain shape. Collectively, our findings provided a theoretical basis and genetic resources for the cloning, functional analysis, and molecular breeding of genes related to rice grain shape.

High-density GBS-based genetic linkage map construction and QTL identification associated with leaf cuticular wax, adaxial stomatal density and leaf water retention capacity in banana

The drought tolerance quantitative trait locus (QTL) in Banana has not been studied to date. In this study, the susceptible parent Musa acuminata ssp. burmannicoides Colla –'Calcutta-4' and the resistant parent Musa balbisiana collection 'Bee hee kela' were crossed to produce an F1 mapping population of 96 individuals for the purpose of mapping drought tolerance traits in banana. Consequently, an entirely novel mapping population was developed using progenitor lines with distinct genomic compositions (A genome and B genome). We employed, the GBS (Genotype By Sequencing) technique to develop a genetic linkage map. The map contained a total of 1015 SNP markers, 11 linkage groups, and a total distance of 4828.88cM. The average distance between markers was 4.9cm. The two primary methods that a plant loses water are through stomata and cuticle transpiration, both of which is not beneficial for the plant. Thus, in the present investigation, the AB mapping population's adaxial stomatal count is measured using a microscopic technique, and leaf cuticular wax was estimated using a spectroscopic method. In addition, the leaf's water retention capacity was estimated. Genetic analysis showed that the drought tolerance traits exhibited moderate to moderately high PCV, GCV, and GAM values, as well as high heritability. Using the GBS-based genetic linkage map and phenotyping information, the QTL analysis identified five main QTLs for drought tolerance on chromosomes 2, 5, and 8. They were designated as wax13_1, wax15_1, wax15_2, lwrc_1, and asd_1. The PVE (per cent) of the identified QTLs varied between 15.9 and 19.8 percent. To our knowledge, this is the first report on the employing of SNP markers to identify QTLs associated with drought tolerance traits in banana. This study's findings will be helpful in fine-mapping and marker-assisted selection in banana for drought related traits.

Construction of the first high-density genetic linkage map and QTL mapping of flavonoid and leaf-size related traits in Epimedium

BackgroundLeaves are the main medicinal organ in Epimedium herbs, and leaf flavonoid content is an important criterion of Epimedium herbs. However, the underlying genes that regulate leaf size and flavonoid content are unclear, which limits the use of breeding for Epimedium development. This study focuses on QTL mapping of flavonoid and leaf-size related traits in Epimedium.ResultsWe constructed the first high-density genetic map (HDGM) using 109 F1 hybrids of Epimedium leptorrhizum and Epimedium sagittatum over three years (2019–2021). Using 5,271 single nucleotide polymorphism (SNP) markers, an HDGM with an overall distance of 2,366.07 cM and a mean gap of 0.612 cM was generated by utilizing genotyping by sequencing (GBS) technology. Every year for three years, 46 stable quantitative trait loci (QTLs) for leaf size and flavonoid contents were discovered, including 31 stable loci for Epimedin C (EC), one stable locus for total flavone content (TFC), 12 stable loci for leaf length (LL), and two stable loci for leaf area (LA). For flavonoid content and leaf size, the phenotypic variance explained for these loci varied between 4.00 and 16.80% and 14.95 and 17.34%, respectively.ConclusionsForty-six stable QTLs for leaf size and flavonoid content traits were repeatedly detected over three years. The HDGM and stable QTLs are laying the basis for breeding and gene investigation in Epimedium and will contribute to accelerating the identification of desirable genotypes for Epimedium breeding.

Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin

BackgroundTaraxacum kok-saghyz Rodin (TKS) is a promising commercial alternative natural rubber (NR) yielding plant. Cultivating TKS with a high NR content is an important breeding target, and developing molecular markers related to NR content can effectively accelerate the breeding process of TKS.ResultsTo construct a high-density SNP genetic map and uncover genomic regions related to the NR content in TKS, an F1 mapping population of TKS was constructed by crossing two parents (l66 and X51) with significant differences in NR contents. The NR content of the F1 plants ranged from 0.30 to 15.14% and was distributed normally with a coefficient of variation of 47.61%, indicating quantitative trait inheritance. Then, employing whole-genome resequencing (WGR), a TKS genetic linkage map of 12,680 bin markers comprising 322,439 SNPs was generated. Based on the genetic map and NR content of the F1 population, six quantitative trait loci (QTLs) for NR content with LOD > 4.0 were identified on LG01/Chr01 and LG06/Chr06. Of them, the 2.17 Mb genomic region between qHRC-C6-1 and qHRC-C6-2 on ChrA06, with 65.62% PVE in total, was the major QTL region. In addition, the six QTLs have significant additive genetic effects on NR content and could be used to develop markers for marker-assisted selection (MAS) in TKS with a high NR content.ConclusionThis work constructed the first high-density TKS genetic map and identified the QTLs and genomic regions controlling the NR content, which provides useful information for fine mapping, map-based cloning, and MAS in TKS.

Specific-Locus Amplified Fragment Sequencing (SLAF-Seq).

Specific length amplified fragment sequencing (SLAF-seq) technology is a simplified genome sequencing technology based on next-generation sequencing. SLAF-seq technology has several distinguishing characteristics: 1. Deep sequencing to ensure accuracy of genotyping; 2. Effectively reduce sequencing costs; 3. Pre-designed simplified representation scheme to optimize marker efficiency; 4. Doubled barcode system for large populations. The advantages and technical process of SLAF-seq are described briefly with summarized results for the application of SLAF-seq in development of molecular markers, construction of high-density genetic map and gene mapping in ornamental plants. Finally, the difficulties and prospects of this method are discussed in application.

Construction of High-Density Genetic Linkage Map Using GBS-SNPs and SSRs in Interspecific Hybrid Derived from the Cross Between ‘Manpungbae’ and ‘Oharabeni’ Pear (Pyrus spp.)

Construction of High-Density Genetic Linkage Map Using GBS-SNPs and SSRs in Interspecific Hybrid Derived from the Cross Between ‘Manpungbae’ and ‘Oharabeni’ Pear (<i>Pyrus</i> spp.)

Construction of SNP-Based High-Density Genetic Map Using Genotyping by Sequencing (GBS) and QTL Analysis of Growth Traits in Eucommia ulmoides Oliver

Eucommia ulmoides Oliv. (2n = 34), native to China and of a monotypic family and genus, is a multipurpose tree species with high economic, ecological, and social benefits. In this study, an F1 population of 109 progenies and tow parents were used to construct the first high-density genetic map of E. ulmoides via genotyping-by-sequencing (GBS) with single-nucleotide polymorphism (SNP) markers. A total of 191,095 SNPs were obtained, among which the available markers in F1 population were types “hkxhk,” “nnxnp,” and “lmxll” and the three polymorphic markers 35,699, 65,800, and 68,022, respectively. Finally, the map comprised 10,103 SNP markers distributed on 17 linkage groups (LGs) that were consisted with the chromosome haploid number in E. ulmoides (n = 17). The interval genetic map covered 90% of the E. ulmoides genomes, with total genetic distance of 4051.11 cM and average distance between markers of 0.45 cM. The length of LGs varied from 70.42 to 495.49 cM, with the mean size of 238.3 cM. On the other hand, 44 QTLs associated with growth traits were detected on LG02, LG06, LG07, LG08, and LG10, with phenotypical variance ranging from 10.0% to 14.2%. A total of 33 candidate genes were identified, and most of them were related to energy storage, signal transmission, hormones, and metabolic pathways. This study could provide a solid foundation for chromosome assembly and refinement, and the localization of growth-trait QTLs will advance the investigation of forestry breeding efforts in E. ulmoides.

Construction of A GBS-Based High-Density Genetic Map and Flower Color-Related Loci Mapping in Grasspea (Lathyrus sativus L.).

Grasspea (Lathyrus sativus L.), a legume crop with excellent resistance to a broad array of environmental stressors, has, to this point, been poorly genetically characterized. High-density genetic linkage maps are critical for draft genome assembly, quantitative trait loci (QTLs) analysis, and gene mining. The lack of a high-density genetic linkage map has limited both genomic studies and selective breeding in grasspea. Here, we developed a high-density genetic linkage map of grasspea using genotyping-by-sequencing (GBS) to sequence 154 grasspea plants, comprising 2 parents and 152 F2 progeny. In all, 307.74 Gb of data was produced, including 2,108,910,938 paired-end reads, as well as 3536 SNPs mapped to seven linkage groups (LG1–LG7). With an average length of 996.52 cM per LG, the overall genetic distance was 6975.68 cM. Both the χ2 test and QTL analysis, based on the Kruskal–Wallis (KW) test and interval mapping (IM) analysis, revealed the monogenic inheritance of flower color in grasspea, with the responsible QTL located between 308.437 cM and 311.346 cM in LG4. The results can aid grasspea genome assembly and accelerate the selective breeding of new grasspea germplasm resources.

Construction of High-Density Genetic Map and Identification of a Bruchid Resistance Locus in Mung Bean (Vigna radiata L.).

Mung bean (Vigna radiata L.) is an economically important grain legume cultivated in Asian countries. High-density genetic linkage is a valuable and effective tool for mapping quantitative trait loci (QTL). In the current study, a high-resolution genetic map containing 4,180 single-nucleotide polymorphisms (SNPs) was assigned to 11 linkage groups (LGs) and spanning 1,751.39 cM in length was constructed for mung bean, and the average distance between adjacent markers was 0.42 cM. Bruchids (Callosobruchus spp.) cause significant damage to and loss of legume seeds. A locus for bruchid resistance was detected. The gene Vradi05g03810, encoding a probable resistance-specific protein, was found to be the most likely key candidate gene in mung beans. A 69-bp sequence deletion was identified in the coding region by comparing the cDNA sequences of bruchid-resistant and bruchid-susceptible lines. This SNP-based high-density linkage map is one of the first to be constructed across the mung bean genome. This map will not only facilitate the genetic mapping of genes or complex loci that control important agronomic traits but also offer a tool for promoting future genetics and comparative genomic studies in Vigna.

Construction of high-density genetic linkage map and QTL mapping for growth performance in black carp (Mylopharyngodon piceus)

Growth related traits controlled by quantitative trait loci (QTL) are important economic traits in aquaculture fish species. In order to dissect these QTL, a high-density genetic linkage map is particularly important. In this study, the first high-density genetic linkage map of black carp ( Mylopharyngodon piceus ) was constructed using one F 1 family comprising of 128 progenies, based on genotyping-by-sequencing (GBS). A total of 10,390 single nucleotide polymorphisms (SNPs) were discovered and genotyped. A number of 4108 high-quality SNPs were assigned to 24 linkage groups (LGs) and the total length of the map was 1708.53 cM with a resolution of 0.51 cM. Conserved syntenic relationship between the high-density linkage map and the zebrafish chromosomes was detected. Relying on this high-density linkage map, 17 suggestive QTL: one for body weight, four for body length, six for body height, and six for body wide, were identified on three linkage groups (LG10, LG17, LG20). The phenotypic variance explained (PVE) by these QTL ranged from 10.9 to 15.5%. The high-density genetic linkage map serves as valuable genomic resources not only for understanding the genomic basis of economically important traits in this fish species, but also for comparative genomics and evolutionary studies of black carp. The identified QTL provide important value for ongoing marker assisted selection (MAS) in this fish. • The first genetic linkage map for black carp with an average resolution of 0.51 cM per locus was constructed using 4197 SNPs • 17 QTL related to body weight, body length, body width and body height were identified on three linkage groups • The LG1 in black carp corresponding to Chr10 and Chr22 in zebrafish genome.

High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping QTLs of Resistance to Aspergillus flavus Infection in Peanut.

The cultivated peanut (Arachis hypogaea L.), which is rich in edible oil and protein, is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanuts, hindering the development of the peanut industry and threatening the health of consumers. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for the control of aflatoxin contamination, and understanding the genetic basis of resistance is vital to its genetic enhancement. In this study, we reported the quantitative trait locus (QTL) mapping of resistance to A. flavus infection of a well-known resistant variety, J11. A mapping population consisting of 200 recombinant inbred lines (RILs) was constructed by crossing a susceptible variety, Zhonghua 16, with J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of an infection index in 4 consecutive years, six novel resistant QTLs with 5.03–10.87% phenotypic variances explained (PVE) were identified on chromosomes A05, A08, B01, B03, and B10. The favorable alleles of five QTLs were from J11, while that of one QTL was from Zhonghua 16. The combination of these favorable alleles significantly improved resistance to A. flavus infection. These results could contribute greatly to the understanding of the genetic basis of A. flavus resistance and could be meaningful in the improvement of further resistance in peanuts.

Construction of high-density SNP genetic maps and QTL mapping for dwarf-related traits in Litchi chinensis Sonn

Litchi chinensis Sonn is widely cultivated in subtropical regions and has an important economic value. A high-density genetic map is a valuable tool for mapping quantitative trait loci (QTL) and marker-assisted breeding programs. In this study, a single nucleotide polymorphism (SNP)-based high-density linkage map was constructed by a genotyping-by-sequencing (GBS) protocol using an F1 population of 178 progenies between two commercial litchi cultivars, ‘Ziniangxi’ (dwarf) and ‘Feizixiao’ (vigorous). The genetic map consisted of 3027 SNP markers with a total length of 1711.97 cM in 15 linkage groups (LGs) and an average marker distance of 0.57 cM. Based on this high-density linkage map and three years of phenotyping, a total of 37 QTLs were detected for eight dwarf-related traits, including length of new branch (LNB), diameter of new branch (DNB), length of common petiole (LCP), diameter of common petiole (DCP), length of internode (LI), length of single leaf (LSL), width of single leaf (WSL), and plant height (PH). These QTLs could explain 8.0 to 14.7% (mean=9.7%) of the phenotypic variation. Among them, several QTL clusters were observed, particularly on LG04 and LG11, which might show enrichment for genes regulating the dwarf-related traits in litchi. There were 126 candidate genes identified within the QTL regions, 55 of which are differentially expressed genes by RNA-seq analysis between ‘Ziniangxi’ and ‘Feizixiao’. These DEGs were found to participate in the regulation of cell development, material transportation, signal transduction, and plant morphogenesis, so they might play important roles in regulating plant dwarf-related traits. The high-density genetic map and QTLs identification related to dwarf traits can provide a valuable genetic resource and a basis for marker-assisted selection and genomic studies of litchi.

Construction of high-density genetic map and QTL mapping in Nicotiana tabacum backcrossing BC4F3 population using whole-genome sequencing

Backcrossing is a powerful tool for plant breeding. The improved marker-assisted backcrossing intends to transfer targeted genes or quantitative trait loci (QTLs) of interest from a donor parent into a recurrent parent. In this study, a tobacco BC4F3 population was generated using Y3 and K326 as hybrid parents and YF1-1 as F&lt;sub&gt;1&lt;/sub&gt; parents. High-throughput sequencing data of 381 pedigree populations were used to construct high-density genetic maps containing 24 142 high-quality single nucleotide polymorphism (SNP) markers with an average genetic distance of 0.59 cM. A genome module analysis was then performed for all the offspring. A total of forty-three candidate QTLs for six agronomics traits were identified. This study provides original biomarkers for tobacco breeding and offers clues for prospective backcrossing applications in other plants.

High-Density GBS-Based Genetic Linkage Map Construction and QTL Identification Associated With Yellow Mosaic Disease Resistance in Bitter Gourd (Momordica charantia L.).

Yellow mosaic disease (YMD) in bitter gourd (Momordica charantia) is a devastating disease that seriously affects its yield. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to YMD has not yet been reported. With the objective of mapping YMD resistance in bitter gourd, the susceptible parent “Punjab-14” and the resistant parent “PAUBG-6” were crossed to obtain F4 mapping population comprising 101 individuals. In the present study, the genotyping by sequencing (GBS) approach was used to develop the genetic linkage map. The map contained 3,144 single nucleotide polymorphism (SNP) markers, consisted of 15 linkage groups, and it spanned 2415.2 cM with an average marker distance of 0.7 cM. By adopting the artificial and field inoculation techniques, F4:5 individuals were phenotyped for disease resistance in Nethouse (2019), Rainy (2019), and Spring season (2020). The QTL analysis using the genetic map and phenotyping data identified three QTLs qYMD.pau_3.1, qYMD.pau_4.1, and qYMD.pau_5.1 on chromosome 3, 4, and 5 respectively. Among these, qYMD.pau_3.1, qYMD.pau_4.1 QTLs were identified during the rainy season, explaining the 13.5 and 21.6% phenotypic variance respectively, whereas, during the spring season, qYMD.pau_4.1 and qYMD.pau_5.1 QTLs were observed with 17.5 and 22.1% phenotypic variance respectively. Only one QTL qYMD.pau_5.1 was identified for disease resistance under nethouse conditions with 15.6% phenotypic variance. To our knowledge, this is the first report on the identification of QTLs associated with YMD resistance in bitter gourd using SNP markers. The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for disease resistance.

A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame.

The seed-bearing capsule of sesame shatters at harvest. This wildish trait makes the crop unsuitable for mechanized harvesting and also restricts its commercial potential by limiting the cultivation for countries that have no access to low-cost labor. Therefore, the underlying genetic basis of the capsule shattering trait is highly important in order to develop mechanization-ready varieties for sustainable sesame farming. In the present study, we generated a sesame F2 population derived from a cross between a capsule shattering cultivar (Muganli-57) and a non-shattering mutant (PI 599446), which was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing. The resulting high-density genetic map contained 782 single-nucleotide polymorphisms (SNPs) and spanned a length of 697.3 cM, with an average marker interval of 0.89 cM. Based on the reference genome, the capsule shattering trait was mapped onto SNP marker S8_5062843 (78.9 cM) near the distal end of LG8 (chromosome 8). In order to reveal genes potentially controlling the shattering trait, the marker region (S8_5062843) was examined, and a candidate gene including six CDSs was identified. Annotation showed that the gene encodes a protein with 440 amino acids, sharing ∼99% homology with transcription repressor KAN1. Compared with the capsule shattering allele, the SNP change and altered splicing in the flanking region of S8_5062843 caused a frameshift mutation in the mRNA, resulting in the loss of function of this gene in the mutant parent and thus in non-shattering capsules and leaf curling. With the use of genomic data, InDel and CAPS markers were developed to differentiate shattering and non-shattering capsule genotypes in marker-assisted selection studies. The obtained results in the study can be beneficial in breeding programs to improve the shattering trait and enhance sesame productivity.

A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander

BackgroundThe Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci.ResultsIn this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively.ConclusionWe constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.

SNP-based high-density genetic map construction and candidate gene identification for fruit quality traits of Dimocarpus longan Lour

Longan is an economically important fruit tree that is cultivated in subtropical regions worldwide. For longan breeding, traits associated with yield and quality are considered desirable. Thus, fine mapping of quantitative trait loci (QTLs) and mining candidate genes for longan fruit yield and quality would benefit longan breeding. In this study, we constructed the first single-nucleotide polymorphism (SNP)-based genetic map of an F1 longan population using restriction site-associated DNA sequencing. A total of 1,464,790,436 clean reads were generated from 200 F1 progeny from ‘Fengliduo’ (female) × ‘Dawuyuan’ (male) and their parents. The overall integrated map contained 8014 SNP markers, which were assigned to 15 linkage groups with a total length of 2873.39 cM, an average distance of 0.36 cM, and 99.96 % of gaps having a genetic distance of <5 cM. Based on two successive years of fruit phenotyping and this high-density linkage map, 17 stable QTLs were identified, including 12 for single fruit weight (SFW) and 5 for edible rate, but no stable QTLs were identified for soluble solid content. Finally, three key candidate genes, namely, Dlo_007693.1 (DlEXP4), Dlo_011045.1 (DlCNR8), and dlo_034894.1 (DlCYP450), for SFW were identified based on RNA sequencing data and quantitative reverse-transcription polymerase chain reaction. In conclusion, this is the first study on the construction of a high-density genetic map of longan using next-generation sequencing based on the largest mapping population. These results provide valuable information for marker-assisted selection breeding and mining of candidate genes related to fruit traits in longan.