Deletion in KRT75L4 linked to frizzle feather in Xiushui Yellow Chickens

Abstract

Bird feathers are the product of interactions between natural and artificial selection. Feather-related traits are important for chicken selection and breeding. Frizzle feather is characterized by the abnormally development of feathers in chickens. In the current study, frizzle feather characteristics were observed in a local breed called Xiushui Yellow Chicken in Jiangxi, China. To determine the molecular mechanisms that underlie frizzle feather in Xiushui Yellow Chicken, four populations of three breeds (Xiushui Yellow Chicken with frizzle feathers, Xiushui Yellow Chicken with normal feathers, Guangfeng White-Ear Yellow Chicken, and Ningdu Yellow Chicken) were selected for whole-genome resequencing. Using a comparative genome strategy and genome-wide association study, a missense mutation (g.5281494A>G) and a 15-bp deletion (g.5285437-5285451delGATGCCGGCAGGACG) in KRT75L4 were identified as candidate mutations associated with frizzle feather in Xiushui Yellow Chicken. Based on genotyping performed in a large Xiushui Yellow Chicken population, the g.5285437-5285451delGATGCCGGCAGGACG mutation in KRT75L4 was confirmed as the putative causative mutation of frizzle feather. These results deepen the understanding of the molecular mechanisms responsible for frizzle feather, as well as facilitating the molecular detection and selection of the feather phenotype in Xiushui Yellow Chickens.

How structural variants shape avian phenotypes: Lessons from model systems

“…Chickens (Chen, Xi, et al, 2022). The same trait is observed in crosses between a heterozygous frizzle rooster and wild-type hens, generated by a 69-bp deletion with autosomal incomplete dominant inheritance in the same gene (Ng et al, 2012).…”

“…Bruders et al, 2020;Domyan et al, 2014;Han et al, 2011;Krishnan & Cryberg, 2019;Krishnan, 2019;Maclary et al, 2023; , 2022). There are many studies, mostly in chickens, that show associations between SVs and feathering phenotypes (Chen, Xi, et al, 2022;Derks et al, 2018;Domyan et al, 2016;Dong et al, 2018;Elferink et al, 2008;Li et al, 2020;Li, Lee, et al, 2021;Mou et al, 2011;Ng et al, 2012;Shen et al, 2023); comb, muff and beard traits (Dorshorst et al, 2015;Guo et al, 2016;Imsland et al, 2012;Moro et al, 2015;Sato et al, 2010;Wang et al, 2017;Wright et al, 2009;Yang et al, 2020Yang et al, , 2021; and egg production (Cui et al, 2006;Huang et al, 2018;Lan et al, 2021;Manoharan et al, 2021;Vinh et al, 2021). Although less common, there are also associations between SVs and behaviour and domestication (Abe et al, 2013;Chen, Bai, et al, 2022;Falker-Gieske et al, 2023;Khatri et al, 2019;Komiyama et al, 2014;Krause et al, 2019;Rubin et al, 2010;Seol et al, 2019;Zhou et al, 2018;…”

“…The IHH gene is completely deleted in Chinese Xingyi Bantam Chickens (Jin et al., 2016), while a complex rearrangement involving deletions and an insertion affects both the IHH and NHEJ1 genes in Japanese bantam chickens (Kinoshita et al., 2020). Additionally, there are instances where identical or nearly identical SVs in the same gene lead to the same phenotype, for example, the frizzle feather trait is caused by a 15‐bp deletion in the KRT75L4 gene in both Kirin Chickens (Dong et al., 2018) and Xiushui Yellow Chickens (Chen, Xi, et al., 2022). The same trait is observed in crosses between a heterozygous frizzle rooster and wild‐type hens, generated by a 69‐bp deletion with autosomal incomplete dominant inheritance in the same gene (Ng et al., 2012).…”

Whole Genome Resequencing Helps Study Important Traits in Chickens

“…Whole genome resequencing in four populations of three chicken breeds identified a missense mutation (g.5281494A>G) and a 15-bp deletion (g.5285437-5285451delGATGCCGGCAGGACG) in KRT75L4 as candidate gene and mutations in Xiushui yellow chickens through comparative genomics and GWAS analysis to determine the molecular mechanism of frizzle feathers [ 21 ]. Moreover, two candidate mutations were confirmed in a large Xiushui yellow chicken population, and a 15-bp deletion in KRT75L4 was identified as the putative causative mutation of the frizzle feather [ 21 ]. Three independent selection signal analyses of Qilin chickens showed that the GGA33:1.17M-1.39M region was a significant selection region shared by the three detection methods based on whole genome resequencing data [ 46 ].…”

Artificial selection footprints in domestic chicken genomes

“…Indeed, many studies have been done to reveal artificial selection signatures on commercial broilers and layers (Rubin, et al 2010; Elferink, et al 2012; Qanbari, et al 2012; Fan, et al 2013; Gheyas, et al 2015; Boschiero, et al 2018; Qanbari, et al 2019) as well as on indigenous chickens (Guo, et al 2016; Wang, et al 2016; Wang, et al 2017; Zhang, Yang, et al 2017; Bortoluzzi, et al 2018; Lawal, et al 2018; Wang, Li, et al 2020). These studies have identified genes or quantitative trait loci (QTLs) related to specific traits such as body size (Kerje, et al 2003; McElroy, et al 2006; Wang, et al 2016; Wang, et al 2017; Wang, Bu, et al 2020; Wang, Cao, et al 2020; Zhang, et al 2020; Wang, Hu, et al 2021), meat quality (Jennen, et al 2005; Bihan-Duval, et al 2018; Moreira, et al 2018), egg production (Zhao, et al 2021), feathering (Zhao, et al 2016; Guo, et al 2018; Zhang, et al 2018; Yang, et al 2019; Bortoluzzi, et al 2020; Li, Lee, et al 2020; Chen, et al 2022; Qiu, et al 2022), plumage color (Zhang, Liao, et al 2017; Huang, Pu, et al 2020; Huang, Otecko, et al 2020; Nie, et al 2021), skin color (Li, Sun, et al 2020), behaviors (Luo, et al 2020; Mehlhorn and Caspers 2020), immunity (Zou, et al 2020), crest shapes (Li, Lee, et al 2021), bone traits (Wang, et al 2018; Li, Liu, et al 2021; Kondoh, et al 2022), rumpless trait (Noorai, et al 2012; Freese, et al 2014; Xu, et al 2017; Wang, Khederzadeh, et al 2021), and polydactyly (Zhang, et al 2016; Chu, et al 2017). However, genetic bases of many artificially selected traits, in particular, of indigenous chickens, are far from being fully understood.…”