Microsatellite markers, also known as short tandem repeats (STRs), are important for marker-assisted selection to detect genetic polymorphism, and they are uniformly distributed in eukaryotic genomes. To analyze the relationship between microsatellite loci and lactation traits of Holstein cows in Xinjiang, 175 lactating cows with similar birth dates, the same parity, and similar calving dates were selected, and 10 STR loci closely linked to quantitative trait loci were used to analyze the correlation between each STR locus and four lactation traits (daily milk yield, milk fat percentage, milk protein percentage, and lactose percentage). All loci showed different degrees of genetic polymorphism. The average values of observed alleles, effective alleles, expected heterozygosity, observed heterozygosity, and polymorphic information content of the 10 STR loci were 10, 3.11, 0.62, 0.64, and 0.58, respectively. Chi-square and G-square tests showed that all populations of loci were in accordance with the Hardy–Weinberg equilibrium. Analysis of the correlation between STR locus genotype and lactation performance in the whole lactation period showed three loci (namely, BM143, BM415, and BP7) with no significant correlation with all lactation traits, two loci (BM302 and UWCA9) related to milk yield, three loci (BM103, BM302, and BM6425) related to milk fat percentage, two loci (BM302 and BM6425) related to milk protein percentage, and three loci (BM1443, BM302, and BMS1943) related to lactose percentage. The microsatellite loci selected in this study showed rich polymorphism in the experimental dairy cow population and were related to the lactation traits, which can be used for the evaluation of genetic resources and early breeding and improvement of Holstein dairy cows in Xinjiang.

Mid-infrared spectroscopy (MIRS) is increasingly used as a rapid and effective analytical method for the quantitative prediction of detailed milk composition, such as minerals, fatty acids, and AA. These analyses require the transportation of samples to a certified laboratory. In this case, storage time may affect MIRS and its prediction results. This study aimed to determine the effect of milk storage time on MIRS and its predictions of AA content. A total of 373 individual milk samples for the development of AA content prediction equations were collected from 7 commercial dairy farms (dataset 1), and 103 individual milk samples for the analysis of the effect of storage time were collected from 2 farms (dataset 2). First, separate quantitative prediction models based on dataset 1 were developed for each AA using partial least squares regression; the accuracy of prediction was assessed using a cross-validation set. Second, repeatability and reproducibility of the predictions of AA were calculated using milk samples in dataset 2, whose spectra were measured once a day for 7 consecutive days after sampling storing at 4°C, to assess the effect of storage time on the consistency of MIRS predicted AA content. Moderate to high prediction accuracy of AA was achieved, with the ratio of performance to deviation of the cross-validation set and the R² of the cross-validation set being in the range of 1.59 (Gly) to 2.39 (Leu), and from 0.58 (Gly) to 0.79 (Leu), respectively. Results demonstrated that the absorbance of spectral points was affected by milk storage time, especially in the absorption areas associated with fat, protein, lactose, SCC, urea, and acetone. However, the predictions of all the AA by MIRS were repeatable and reproducible across different milk storage times until 6 d after sampling, except for Tyr, His, and Phe, with repeatability and reproducibility both greater than or close to 90%. In conclusion, for milk stored at 4°C and preserved with bronopol, MIRS can provide relatively consistent and accurate predictions for AA content for 0 to 6 d after milk collection. However, a shorter storage time, such as within 3 d after collection, is recommended when conditions permit.

Background: DNA barcoding, an emerging approach, is being widely used to accurately and quickly identify species using conserved DNA sequences. Methods: Herein we designed seven universal primers for matK (matK1, matK2, matK3 and matK4), rbcL, psbA-trnH and ITS based on their nucleotide sequences in GenBank to amplify 40 species of leguminosae and grass forages. Sequence alignment was performed using MEGA 5.0 and haplotype and mutation sites were analyzed with DnaSP 5.10. PCR amplification efficiency on using the primers designed for psbA-trnH and ITS was relatively low, making these sequences unsuitable for DNA barcoding. Further, we optimized target fragment amplification conditions for all 40 species analyzed in this study. On purifying, sequencing and analysing amplification products, we selected 5′ - and 3′ -end conserved fragments in four marked fragments. Result: Sequences of each maker loci showed that there were 12, 17 and 6 haplotypes of matK1, matK2 and matK3, respectively and 13 of rbcL. Based on these haplotypes of matK1, matK2, matK3 and rbcL, we established a DNA barcoding database for 20 forage species.

The Hetian Gray Donkeys (China_HTQD) and Xinjiang Donkeys (China_XJD) are representative local donkey breeds in Xinjiang, China, that show significant differences in production phenotypes, such as body size and coat color. However, their genetic background and the molecular mechanisms influenced by artificial selection have not been systematically elucidated. This study integrated whole-genome data from 60 newly sequenced China_HTQD and China_XJD individuals, along with 155 global reference datasets from the NCBI database, to construct a modern donkey whole-genome variation set covering domestic and overseas populations (including Africa, West and Central Asia, and Europe). The results of genetic diversity analysis indicated that China_XJD has slightly higher genetic diversity than China_HTQD, while the China reference population (China_Ref) and European population (Europe) have the lowest genetic diversity. China_HTQD and China_XJD have greater genetic variation. Both PCA and NJ phylogenetic analyses showed that China_HTQD and China_XJD are genetically very close, clustering within the Chinese donkey population background, and exhibit clear geographic genetic isolation from overseas reference populations. ADMIXTURE analysis (with K = 2 showing the lowest cross-validation error) revealed that the two breeds share a highly similar genetic structure, with only minor differences in the proportions of specific ancestral components, while both are distinctly different from the other four reference populations. A whole-genome differentiation scan (F_st) showed limited overall genetic differentiation between China_HTQD and China_XJD populations, but significant differentiation peaks were observed in some genomic regions. Based on the joint screening of windowed F_st (Fixation Index) and XP-CLR (Cross-Population Composite Likelihood Ratio), this study identified two candidate genomic regions containing the TBX3 and ZFAT genes. Among these, TBX3 emerged as a strong candidate with a robust selection signal and a well-established role in body size regulation. In contrast, ZFAT showed a weaker signal, and its potential involvement in coat color remains speculative and requires further validation. In summary, this study not only clarified the close genetic relationship and the level of interpopulation differentiation between China_HTQD and China_XJD at the whole-genome level but also identified candidate genes potentially associated with phenotypic divergence, providing gene-level confirmation of TBX3 and the novel identification of ZFAT as a candidate for coat-color variation, thereby providing a scientific foundation for elucidating the genetic mechanisms underlying phenotypic differences in Xinjiang’s local donkey genetic resources.

Camel milk is rich in nutrients and bioactive factors, which are crucial for human nutrition, health, and disease treatment. However, there is limited research on the genes related to lactation traits in Bactrian camels and their regulatory mechanisms. This lack of research prevents the provision of systematic molecular breeding guidance to improve milk production traits and enhance milk quality in Bactrian camels. Previous research has shown a significant difference in milk production traits between the eastern and northern regions of Xinjiang. In this study, 106 Bactrian camels were collected—55 from three camel farms in the northern region and 51 from one farm in the eastern region—for whole-genome resequencing. Through variant detection, population structure, and selection signal analysis, a total of 6,451,453 SNPs were identified. Principal component analysis and phylogenetic tree analysis revealed that the Bactrian camel populations from the eastern and northern regions can be clearly distinguished. GO analysis and KEGG enrichment analysis revealed that, compared to Bactrian camels from the northern region, candidate genes from the eastern region were mainly enriched in two pathways: plasma membrane and thyroid hormone synthesis. Whole-genome selection signal analysis identified eight candidate genes potentially related to lactation traits: DUOX1, DUOX2, CPQ, CGA, PLCG1, FYN, GNRHR, and TRHR. These genes can serve as potential marker sites for molecular breeding in the future.