São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil.
Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil.
BMC Genomics. 2020 Sep 29;21(1):672. doi: 10.1186/s12864-020-07090-z.
Pacu (Piaractus mesopotamicus) is one of the most important Neotropical aquaculture species from South America. Disease outbreaks caused by Aeromonas hydrophila infection have been considered significant contributors to the declining levels of pacu production. The current implementation of genomic selection for disease resistance has been adopted as a powerful strategy for improvement in fish species. This study aimed to investigate the genetic architecture of resistance to A. hydrophila in pacu via Genome-Wide Association Study (GWAS), the identification of suggestive Quantitative Trait Loci (QTLs) and putative genes associated with this trait. The genetic data were obtained from 381 juvenile individuals belonging to 14 full-sibling families. An experimental challenge was performed to gain access to the levels of genetic variation for resistance against the bacteria using the following trait definitions: binary test survival (TS) and time of death (TD).
The analyses of genetic parameters estimated moderate heritability (h) for both resistance traits: 0.20 (± 0.09) for TS and 0.35 (± 0.15) for TD. A linkage map for pacu was developed to enable the GWAS, resulting in 27 linkage groups (LGs) with 17,453 mapped Single Nucleotide Polymorphisms (SNPs). The length of the LGs varied from 79.95 (LG14) to 137.01 (LG1) cM, with a total map length of 2755.60 cM. GWAS identified 22 putative QTLs associated to A. hydrophila resistance. They were distributed into 17 LGs, and were considered suggestive genomic regions explaining > 1% of the additive genetic variance (AGV) for the trait. Several candidate genes related to immune response were located close to the suggestive QTLs, such as tbk1, trim16, Il12rb2 and lyz2.
This study describes the development of the first medium density linkage map for pacu, which will be used as a framework to study relevant traits to the production of this species. In addition, the resistance to A. hydrophila was found to be moderately heritable but with a polygenic architecture suggesting that genomic selection, instead of marker assisted selection, might be useful for efficiently improving resistance to one of the most problematic diseases that affects the South American aquaculture.
亚马逊油鲇（Piaractus mesopotamicus）是南美洲最重要的水产养殖新热带鱼类之一。由嗜水气单胞菌感染引起的疾病爆发已被认为是导致亚马逊油鲇产量下降的重要因素。目前，通过基因组选择来提高鱼类的抗病性已成为一种强有力的策略。本研究旨在通过全基因组关联研究（GWAS）来研究亚马逊油鲇对嗜水气单胞菌的抗性遗传结构，鉴定与该性状相关的推定数量性状基因座（QTL）和候选基因。遗传数据来自 14 个全同胞家系的 381 只幼鱼。通过对细菌的抗性进行实验性挑战，获得了用于抵抗细菌的遗传变异水平的以下性状定义：二元测试生存（TS）和死亡时间（TD）。
所估计的遗传参数分析表明，两种抗性性状均具有中度遗传力（h）：0.20（±0.09）用于 TS，0.35（±0.15）用于 TD。为了进行 GWAS，开发了一个亚马逊油鲇的连锁图谱，得到了 27 个连锁群（LGs），有 17453 个映射的单核苷酸多态性（SNP）。LG 长度从 79.95（LG14）到 137.01（LG1）厘摩不等，总图谱长度为 2755.60 厘摩。GWAS 鉴定出 22 个与嗜水气单胞菌抗性相关的推定 QTL。它们分布在 17 个 LG 中，被认为是解释该性状 >1%加性遗传方差（AGV）的基因组区域。一些与免疫反应相关的候选基因位于推定 QTL 附近，如 tbk1、trim16、Il12rb2 和 lyz2。
本研究描述了第一个用于亚马逊油鲇的中密度连锁图谱的开发，该图谱将被用作研究与该物种生产相关的性状的框架。此外，嗜水气单胞菌的抗性被发现具有中度遗传力，但具有多基因遗传结构，这表明基因组选择而不是标记辅助选择可能有助于有效提高对影响南美洲水产养殖的最严重疾病之一的抗性。
