Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)

Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits.

Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)

Background Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between ‘Criollo de Morellos-334’ (CM-334), a resistant landrace from Mexico, and ‘Early Jalapeno’, a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. Results Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. Conclusions Results support the genetic complexity of the P. capsici–Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio)

Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9–15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.

Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Allium cepa L.)

Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F2 segregating population derived from a cross between the doubled haploid line ‘16P118′ and inbred line ‘Sweet Green’ through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (qSC4.1), glucose (qGC5.1), fructose (qFC5.1), and total sugar content (qTSC5.1) explaining the phenotypic variation (R2%) ranging from 6.07–11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.