Variation in the Caprine Keratin-Associated Protein 27-1 Gene is Associated with Cashmere Fiber Diameter

Abstract

Variation in some caprine keratin-associated protein (KAP) genes has been associated with cashmere fiber traits, but many KAP genes remain unidentified in goats. In this study, we confirm the identification of a KAP27-1 gene (KRTAP27-1) and describe its effect on cashmere traits in 248 Longdong cashmere goats. A polymerase chain reaction–single strand conformation polymorphism (PCR-SSCP) analysis was used to screen for sequence variation in this gene, and three sequence variants (named A to C) were found. These sequences have the highest similarity (77% identity) to a human KRTAP27-1 sequence, while sharing some homology with a predicted caprine KRTAP27-1 sequence ENSCHIG00000023347 in the goat genome construct (ARS1:CM004562.1) at chromosome 1 position 3,966,193–3,973,677 in the forward strand. There were two single nucleotide polymorphisms (SNPs) detected in the coding sequence, including one nonsynonymous SNP (c.413C/T; p.Ala138Val) and one synonymous SNP (c.495C/T). The C variant differed from A and B at c.413C/T, having cytosine in its nucleotide sequence, while the B variant differed from A and C at c.495C/T, having thymine in its nucleotide sequence. Goats of the genotypes AB and BB produced cashmere fibers of higher mean fiber diameter (MFD) than goats of genotype AA, but no difference in MFD was detected between the AB and BB goats. These results suggest that B is associated with increased MFD. Expression of the caprine KRTAP27-1 sequence was predominantly detected in the skin tissue of goats but not or only weakly detected in other tissues, including longissimus dorsi muscle, heart, kidney, liver, lung and spleen.

The Complexity of the Ovine and Caprine Keratin-Associated Protein Genes

“…This suggests gene conversion or non-reciprocal genetic exchange is one of the mechanisms for creating sequence diversity in some KRTAP s. Unique sequence motifs have been postulated to promote genetic recombination, including the crossover hotspot instigator (Chi) sequence (5′-GCTGGTGG-3′) or its complementary sequence, which are abundant in the genomes of bacteriophage and Escherichia coli [ 83 ]. Chi and Chi-like sequences, or their complementary sequences, have been reported in KRTAP s [ 19 , 61 , 64 , 65 ]. It is proposed that Chi-like sequences, with minor nucleotide variations to the consensus Escherichia coli Chi sequence, may have partial ‘hotspot’ activity [ 84 ].…”

Variation in a Newly Identified Caprine KRTAP Gene Is Associated with Raw Cashmere Fiber Weight in Longdong Cashmere Goats

“…There is literature reporting Chi or Chi-like sequences in KRTAPs from sheep and goats, including as ovine KRTAP1-n [ 17 ], ovine KRTAP15-1 [ 28 ], caprine KRTAP15-1 [ 6 ], caprine KRTAP24-1 [ 7 ] and caprine KRTAP27-1 [ 9 ]. Chi (crossover hotspot instigator, χ) is an octamer motif (5’-GCTGGTGG-3’) that has been described as a recombination hotspot in E. coli and related to the recombination of double-strand DNA breaks sites [ 29 ].…”

“…Over the last four decades, the identification of KRTAPs and research into the effect of these genes on hair and wool traits has been most commonly focused on humans and sheep. However, to date, only 17 KRTAPs have been identified from 13 families in goats [ 5 , 6 , 7 , 8 , 9 ].…”

“…The genetic similarity between sheep and goats suggests that many KRTAPs remain to be identified in the goat genome. Of the 17 caprine KRTAPs identified to date, seven of them have been reported to affect cashmere fiber length, cashmere fiber yield and cashmere mean fiber diameter, including KRTAP8-2 [ 10 ], KRTAP20-2 [ 11 ], KRTAP20-1 [ 12 ], KRTAP15-1 [ 6 ], KRTAP27-1 [ 9 ], KRTAP28-1 [ 8 ] and KRTAP24-1 [ 7 ]. This suggests that nucleotide sequence variation in the caprine KRTAPs is an important determinant of key cashmere traits.…”

Sequence Variation in Caprine KRTAP6-2 Affects Cashmere Fiber Diameter

“…While 88 functional KRTAPs from 25 families have been identified in humans, and 30 KRTAPs comprised of 18 families have been reported in sheep, only 18 KRTAPs and 12 families having been identified in goats [ 6 ]. Of the 18 caprine KRTAPs identified, variation in 10 of these genes has been reported to be associated with selected cashmere fiber traits, including KRTAP1-3 [ 7 ], KRTAP8-2 [ 8 ], KRTAP9-2 [ 9 ], KRTAP13-1 [ 10 ], KRTAP15-1 [ 11 ], KRTAP20-1 [ 12 ], KRTAP20-2 [ 1 ], KRTAP24-1 [ 13 ], KRTAP27-1 [ 14 ], and KRTAP28-1 [ 15 ].…”