[1]盛欣,徐宇辉,郑文骞,等.四个牛族物种染色体水平基因组完全型微卫星分布特征分析[J].江苏农业学报,2026,42(01):110-119.[doi:doi:10.3969/j.issn.1000-4440.2026.01.012]
　SHENG Xin,XU Yuhui,ZHENG Wenqian,et al.Microsatellite distribution characteristics in chromosome-level genomes of four bovini species[J].,2026,42(01):110-119.[doi:doi:10.3969/j.issn.1000-4440.2026.01.012]
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四个牛族物种染色体水平基因组完全型微卫星分布特征分析()

江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
42
期数:
2026年01期
页码:
110-119
栏目:
畜牧兽医·水产养殖
出版日期:
2026-01-31

文章信息/Info

Title:
Microsatellite distribution characteristics in chromosome-level genomes of four bovini species
作者:
盛欣1; 2; 3; 徐宇辉1; 2; 3; 郑文骞1; 2; 3; 陈生梅1; 2; 3; 李瑞哲1; 2; 3; 王贵元4; 马志杰1; 2; 3
(1.青海大学畜牧兽医科学院,青海西宁810016；2.农业农村部青藏高原畜禽遗传育种重点实验室,青海西宁810016；3.青海省高原家畜遗传资源保护与创新利用重点实验室,青海西宁810016；4.天峻县畜牧兽医站,青海海西817200)
Author(s):
SHENG Xin1; 2; 3; XU Yuhui1; 2; 3; ZHENG Wenqian1; 2; 3; CHEN Shengmei1; 2; 3; LI Ruizhe1; 2; 3; WANG Guiyuan4; MA Zhijie1; 2; 3
(1.Academy of Animal Science and Veterinary, Qinghai University, Xining 810016, China；2.Key Laboratory of Livestock and Poultry Genetics and Breeding on the Qinghai-Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining 810016, China；3.Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining 810016, China；4.Tianjun Animal Husbandry and Veterinary Station, Haixi 817200, China)
关键词:
牛族; 基因组; 完全型微卫星(P-SSR); 丰度; 分布规律
Keywords:
bovini; genome; perfect microsatellites (P-SSRs); abundance; distribution pattern
分类号:
S823
DOI:
doi:10.3969/j.issn.1000-4440.2026.01.012
文献标志码:
A
摘要:
牛族物种作为农业生产与生态系统中的关键类群,其遗传资源的保护与可持续利用对畜牧业发展及维持生物多样性具有重要意义。然而,当前针对牛族物种基因组中完全型微卫星(Perfect microsatellites, P-SSR)的系统比较研究相对匮乏。本研究基于染色体水平的高质量基因组序列,采用Krait v1.4.0软件对普通牛、牦牛(含家牦牛和野牦牛)、瘤牛、水牛基因组中的P-SSR进行系统检测与综合分析。分别从普通牛、家牦牛、野牦牛、瘤牛及水牛全基因组中鉴定出817 477个、775 897个、740 044个、739 975个、777 401个P-SSR；其中,普通牛基因组中P-SSR相对频率最高,其次是水牛、野牦牛和瘤牛,家牦牛基因组中P-SSR相对频率最低。在水牛基因组中,P-SSR序列总长度所占比例最高,普通牛、家牦牛及野牦牛次之,瘤牛最低。在4个牛族物种的基因组中,单核苷酸重复类型P-SSR的出现频率最高,其次为二核苷酸重复、三核苷酸重复、五核苷酸重复、四核苷酸重复、六核苷酸重复。4个牛族物种的单核苷酸重复至五核苷酸重复类型的P-SSR优势重复基序相同,分别为A、AC、AGC、AAAT和AACTG。在各牛族物种中,相同重复类型的P-SSR重复基序数量分布区间高度一致。单核苷酸重复至六核苷酸重复类型的重复基序数量分布范围分别是12～28次、7～24次、5～13次、4～8次、4～7次和4～10次。相关性分析结果表明,4个牛族物种基因组中各条染色体长度与其所含P-SSR数量呈极显著正相关（P<0.001）,而各条染色体P-SSR相对频率和相对密度均与其染色体G+C含量呈显著或极显著负相关（P<0.05、P<0.01、P<0.001）。长度大于100 bp和1 000 bp的P-SSR数量在家牦牛基因组中最多。综上,本研究结果系统揭示了各牛族物种基因组中P-SSR的丰度与分布规律,为深入探究牛族物种基因组中重复序列的组成差异、进化机制及其生物学功能提供了重要依据。
Abstract:
Bovini species play a crucial role in agricultural production and ecosystem functioning, and the conservation and sustainable utilization of these genetic resources are of great significance for the development of animal husbandry and the maintenance of biodiversity. However, systematic comparative studies on perfect mi-crosatellites (P-SSRs) in the genomes of bovini species are still scarce. To address this gap, this study conducted systematic detection and comprehensive analysis of P-SSRs in cattle (Bos taurus), yak (Bos grunniens and Bos mutus), zebu (Bos indicus), and buffalo (Bubalus bubalis) using Krait v1.4.0 software based on high-quality chromosome-level genome sequences. The results showed that a total of 817 477, 775 897, 740 044, 739 975, and 777 401 P-SSRs were identified in the genomic sequences of cattle, domestic yak, wild yak, zebu and buffalo, respectively. Among them, the P-SSRs showed the highest relative frequency in cattle, followed by buffalo, wild yak, and zebu, with the lowest in domestic yak. Moreover, the proportion of the total length of P-SSRs was the highest in buffalo, followed by cattle, domestic yak, and wild yak, with zebu showing the lowest proportion. In the genomic sequences of the four bovini species, the relative frequency of mononucleotide repeats of SSRs was the highest, followed by dinucleotide, trinucleotide, pentanucleotide, tetranucleotide, and hexanucleotide repeats. In all four bovini species, the dominant repeat motifs of P-SSRs in mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotide repeats were identical, specifically A, AC, AGC, AAAT, and AACTG. Among different bovini species, the distribution ranges of repeat motif counts for each corresponding P-SSR type were highly conserved. The distribution ranges for the number of repeat motifs were 12-28 times for mononucleotide, 7-24 times for dinucleotide, 5-13 times for trinucleotide, 4-8 times for tetranucleotide, 4-7 times for pentanucleotide, and 4-10 times for hexanucleotide repeats. Correlation analysis revealed that across the four bovini species, chromosome length showed a highly significant positive correlation with the number of P-SSRs (P<0.001). In contrast, both the relative frequency and relative density of P-SSRs on each chromosome were significantly or highly significantly negatively correlated with G+C content (P<0.05, P<0.01, P<0.001). The number of P-SSRs longer than 100 bp and 1 000 bp was greatest in the domestic yak genome. In conclusion, the findings of this study systematically reveal the abundance and distribution patterns of P-SSRs in bovini genomes, providing a valuable foundation for further exploration of the compositional divergence, evolutionary mechanisms, and biological functions of repetitive sequences in these species.

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备注/Memo

备注/Memo:
收稿日期：2025-08-18基金项目：青海省“昆仑英才·高端创新创业人才”计划项目(领军人才);第三次全国畜禽遗传资源普查项目作者简介：盛欣(2000-),女,广东汕头人,硕士研究生,主要从事动物遗传资源研究。(E-mail)2603043164@qq.com通讯作者：马志杰,(E-mail)zhijiema@126.com
更新日期/Last Update: 2026-02-09