Genome-Wide Population Structure Analysis and Genetic Diversity Detection of Four Chinese Indigenous Duck Breeds from Fujian Province

Abstract

The assessment of population genetic structure is the basis for understanding the genetic information of indigenous breeds and is important for the protection and management of indigenous breeds. However, the population genetic differentiation of many local breeds still remains unclear. Here, we performed a genome-wide comparative analysis of Jinding, Liancheng white, Putian black, and Shanma ducks based on the genomic sequences using RAD sequencing to understand their population structure and genetic diversity. The population parameters showed that there were obvious genetic differences among the four indigenous breeds, which were separated groups. Among them, Liancheng white and Shanma ducks may come from the same ancestor because the phylogenetic tree forms three tree trunks. In addition, during the runs of homozygosity (ROH), we found that the average inbreeding coefficient of Liancheng white and Putian black ducks was the lowest and the highest, respectively. Five genomic regions were considered to be the hotspots of autozygosity among these indigenous duck breeds, and the candidate genes involved a variety of potential variations, such as muscle growth, pigmentation, and neuroregulation. These findings provide insights into the further improvement and conservation of Fujian duck breeds.

Whole-genome resequencing revealed the population structure and selection signal of 4 indigenous Chinese laying ducks

“…Protecting and effectively utilizing local breed resources are crucial for ensuring the high-quality development of the poultry industry. Actively conducting research on population genetic structure is the foundation for understanding the genetic information of indigenous breeds, and is essential for the effective protection and management of indigenous genetic resources ( Cendron et al, 2020 , Lin et al, 2022 ). The analysis of population structure could help to deepen understanding of species or subspecies formation processes.…”

“…To explore the population structure and selection signals of indigenous laying ducks, we selected 4 laying breeds raised in National Institute of Waterfowl Gene Bank in Fujian Province. Jinding duck ( JD ) is an excellent indigenous laying duck breed in China, and the production area of JD is located in Longhai District of Zhangzhou city, Fujian Province (24°45″ N 117°84″ E) ( Lin et al, 2022 ).The main characteristics of JD are moderate body size (adult female duck about 1.7 kg), brown feather, high proportion of green-shelled eggs (up to 95%), large egg (average egg weight about 72 g), heat and cold resistance, and strong disease resistance. Shanma duck ( SM ) is also an excellent indigenous laying duck, which mainly distributed in Longyan city, Fujian Province (24°09″ N 117°04″ E) ( Feng et al, 2021 ).…”

Identification of relevant differential genes to the divergent development of pectoral muscle in ducks by transcriptomic analysis

“…Liancheng white ducks (LW), a rare local waterfowl breed in China known for its delicious flavor and succulent flesh, were limited due to slow growth and significantly high production cost [ 6 ]. Cherry valley ducks (CV) are a fast-growing breed of large meat duck with disadvantages such as thick subcutaneous fat and poor meat quality [ 7 ].…”