Construction of the first high-density genetic map for growth related QTL analysis in Ancherythroculter nigrocauda

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Construction of the first high-density genetic map for growth related QTL analysis in Ancherythroculter nigrocauda* SUN Yanhong1, 2, #, LI Pei1, 2, #, WANG Guiying1, 2, SUN Renli1, 2, CHEN Jian1, 2, ZHOU Qi3, TONG Jingou4, **, LI Qing1, 2, ** 1

Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China

2

Wuhan Xianfeng Aquaculture Technology Co. Ltd., Wuhan 430207, China

3

Wuhan Academy of Agricultural Sciences, Wuhan 430207, China

4

State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China

Received Nov. 20, 2019; accepted in principle Jan. 26, 2020; accepted for publication Jun. 4, 2020 © Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag GmbH Germany, part of Springer Nature 2020

Abstract Ancherythroculter nigrocauda is a fish endemic to the upper areas of the Changjiang (Yangtze) River in China. Quantitative trait locus (QTL) mapping is a powerful tool to identify potential genes affecting traits of economic importance in domestic animals. In this study, a high-density genetic map was constructed with 5 901 single nucleotide polymorphism (SNP) makers by sequencing 92 individual fish from a F1 family using the specific-locus amplified fragment sequencing approach. Initially, 48 QTLs for total length, body length, body height, and body weight were identified according to the high density of the genetic map with 24 LGs, a total length of 3 839.4 cM, and marker spacing of about 0.82 cM. These QTLs explained 27.1%–49.9% of phenotypic variance. The results of this study suggest that major QTLs are responsible for the growth of A. nigrocauda, and these are potentially useful in comparative genomics research, genome assembly, and marker-assisted breeding programs for this species. Keyword: Ancherythroculter nigrocauda; specific-locus amplified fragment; high-density genetic map; quantitative trait locus

1 INTRODUCTION In aquaculture species, many important traits such as growth, disease resistance, and feed conversion rate have major effects on the productivity and profitability of a species. These traits are generally influenced by a number of quantitative trait loci (QTLs), and most of them have minor effects. However, a few QTLs harbor genes may have major effects that are useful for molecular breeding (Yue, 2014; Tong and Sun, 2015). Traditional strategies of genetic improvement of production traits are based mainly on phenotype and pedigree information, but these strategies require considerable time (Gjedrem, 2000). Genetic linkage maps are considered essential tools for QTL mapping, positional cloning of candidate genes, and anchoring of whole-genome scaffold sequences, which can speed up the genetic improvement of production traits and improve breeding efficiency. A high-density linkage map is

essential for fine QTL mapping, which involves mapping the QTLs in small chromosomal regions and identifying candidate genes in the QTLs. A sufficient number of molecular markers are crucial for