A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach (Paramisgurnus dabryanus)

Abstract

Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.

Identification of Additive–Epistatic QTLs Conferring Seed Traits in Soybean Using Recombinant Inbred Lines

“…Recent advances in sequencing technology have led to the discovery of new markers and the generation of high-density molecular genetic linkage maps to detect 100-SW QTLs for annotated candidate genes in soybean ( Karikari et al, 2019 ). Thus, a high-density molecular genetic map is a basic requirement for QTL fine mapping and candidate gene discovery ( Zhang et al, 2016a ; Wei et al, 2019 ).…”

Peer Review #1 of "Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus (v0.2)"

“…Previous studies have identified sex-related QTLs and genes in fish (Sun et al, 2017;Wei et al, 2019), crabs (Waiho et al, 2019), and shrimps, including L. vannamei and P. monodon (Jones et al, 2020;Wang et al, 2020). In L. vannamei, sex-associated markers were identified on LG42.44 via mapping analysis, and the QTL region supports the ZW-WW chromosomal sex determination system; however, no direct sex determination or differentiation gene could be identified in this research (Jones et al, 2020).…”

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

“…Sexual dimorphism is directly related to the economic benefits of some aquatic species, such as the crabs Scylla paramamosain and Eriocheir sinensis , and the females are preferred because of the yolk; the female Chinese tongue soles ( Cynoglossus semilaevis ) are more preferred owing to their faster growth rate and larger individual size than those of the males. Previous studies have identified sex-related QTLs and genes in fish ( Sun et al, 2017 ; Wei, Chen & Wang, 2019 ), crabs ( Waiho et al, 2019 ; Shi et al, 2018 ), and shrimps, including L. vannamei and P. monodon ( Jones et al, 2020 ; Wang et al, 2020 ). In L. vannamei , sex-associated markers were identified on LG42.44 via mapping analysis, and the QTL region supports the ZW-WW chromosomal sex determination system; however, no direct sex determination or differentiation gene could be identified in this research ( Jones et al, 2020 ).…”