1. The genetic diversity and population structure were studied for eight local chicken breeds, including Anjiyan (AN), Hetian Black (HH), Hetian Ma (HM), Aheqi (AH), Baicheng You (BC), Hejing (HJ), Tashkurghan (TS) and Ruoqiang (RQ), in the Southern Xinjiang region of China, using 20 microsatellite markers. 2. Total 336 alleles were obtained from all chicken breeds, with a mean of 16.8 alleles per locus. The polymorphism information content ranged from 0.444 to 0.911, with a mean of 0.729 and almost all of the loci showed significant deviation from Hardy-Weinberg standards. The observed and expected heterozygosity of the eight breeds ranged from 0.5 to 0.677 and from 0.656 to 0.774, with the lowest observed in the AN and the highest in BC breed. The average breed genetic diversity was 0.655 for AN and 0.766 for BC chickens. 3. According to the neighbour-joining (NJ) method, three main clusters were identified in the NJ phylogenetic tree with AN and RQ breeds in one clade, HH and HM breeds in the second clade and TS, HJ, AH and BC breeds in the third clade. 4. Based on STRUCTURE analysis, the most likely cluster number of all breeds was K=4, whereby HH and HM breeds formed one cluster and AH, BC, HJ, and TS formed another, and RQ, AN chicken formed their own distinct cluster. These results indicated that HH and HM breeds had similar genetic background, as did the breeds of AH, BC, HJ, and TS. RQ, AN breed had unique genetic backgrounds, distinct from the other breeds. Genetic introgression was detected from AN to HH and HM. 5. The results of the current study can be used as baseline genetic information to implement effective conservation programs and to make better use of these local chicken breeds, especially for the AN, RQ, and TS breeds.

To investigate the characteristic aromatic compounds, present in the traditional fermented koumiss of the Kazakh ethnic group in different regions of Xinjiang, GC-IMS, and GC-MS were used to analyze the volatile compounds in koumiss from four regions. A total of 87 volatile substances were detected, and esters, acids, and alcohols were found to be the main aroma compounds in koumiss. While the types of aroma compounds in koumiss were similar across different regions, the differences in their concentrations were significant and displayed clear regional characteristics. The fingerprint spectrum of GC-IMS, combined with PLS-DA analysis, indicates that eight distinctive volatile compounds, including ethyl butyrate, can be utilized to distinguish between different origins. Additionally, we analyzed the OVA value and sensory quantification of koumiss in different regions. We found that aroma components such as ethyl caprylate and ethyl caprate, which exhibit buttery and milky characteristics, were prominent in the YL and TC regions. In contrast, aroma components such as phenylethanol, which feature a floral fragrance, were more prominent in the ALTe region. The aroma profiles of koumiss from the four regions were defined. These studies provide theoretical guidance for the industrial production of Kazakh koumiss products.

Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes - dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 - requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.

Chicken plumage color is an inheritable phenotype that was naturally and artificially selected for during domestication. The Baicheng You chicken is an indigenous Chinese chicken breed presenting three main feather colors, lavender, black, and yellow plumages. To explore the genetic mechanisms underlying the pigmentation in Baicheng You chickens, we re-sequenced the whole genome of Baicheng You chicken with the three plumage colors. By analyzing the divergent regions of the genome among the chickens with different feather colors, we identified some candidate genomic regions associated with the feather colors in Baicheng You chickens. We found that EGR1, MLPH, RAB17, SOX5, and GRM5 genes were the potential genes for black, lavender, and yellow feathers. MLPH, GRM5, and SOX5 genes have been found to be related to plumage colors in birds. Our results showed that EGR1 is a most plausible candidate gene for black plumage, RAB17, MLPH, and SOX5 for lavender plumage, and GRM5 for yellow plumage in Baicheng You chicken.

Introduction: Xinjiang is a region renowned for its rich diversity of native horse breeds, making it one of the most affluent equine genetic resource areas in China. While prized for their high adaptability and tolerance to roughage, the conservation of these native breeds faces challenges from the introduction of external breeds and industrial changes. Furthermore, the unknown population structure of Xinjiang horse breeds has hindered effective conservation efforts. Methods: This study presents the first comprehensive Single Nucleotide Polymorphism (SNP) analysis of seven Xinjiang native horse breeds. We utilized 10X whole-genome sequencing to assess their genetic diversity, population structure, and genetic relationships. Results: Our findings revealed a high level of population genetic diversity among the Xinjiang native horse breeds. These breeds exhibited significant genetic differentiation from other horse breeds originating from Europe, Central Asia, Western Asia, and other parts of China. Evidence of frequent historical gene flow was detected, particularly among breeds in northern Xinjiang, which were shown to be more closely related to each other. Discussion: This study elucidates the distribution patterns, evolutionary characteristics, and substantial genetic diversity of Xinjiang’s native horse breeds. The results provide crucial insights into their unique genetic background and population history. These findings offer valuable theoretical support for establishing core conservation groups of local germplasm, guiding future breeding programs for new cultivars, and further exploration of the characteristics inherent to Xinjiang’s native horse genetic resources.