草业学报 ›› 2021, Vol. 30 ›› Issue (5): 134-145.DOI: 10.11686/cyxb2020212
纪会1,2(), 官久强1, 王会2, 周建旭3, 阿农呷4, 何宗伟5, 樊珍详6, 邱龙康6, 曹诗晓1, 安添午1, 柏琴1, 钟金城2(), 罗晓林1()
收稿日期:
2020-05-12
修回日期:
2020-08-19
出版日期:
2021-05-20
发布日期:
2021-04-16
通讯作者:
钟金城,罗晓林
作者简介:
642163534@qq.com基金资助:
Hui JI1,2(), Jiu-qiang GUAN1, Hui WANG2, Jian-xu ZHOU3, Nong-ga A4, Zong-wei HE5, Zhen-xiang FAN6, Long-kang QIU6, Shi-xiao CAO1, Tian-wu AN1, Qin BAI1, Jin-cheng ZHONG2(), Xiao-lin LUO1()
Received:
2020-05-12
Revised:
2020-08-19
Online:
2021-05-20
Published:
2021-04-16
Contact:
Jin-cheng ZHONG,Xiao-lin LUO
摘要:
亚丁牦牛和拉日马牦牛均为肉乳兼用型优良地方牦牛资源,本研究旨在探究亚丁牦牛和拉日马牦牛的遗传多样性及各牦牛群体间的亲缘关系,对亚丁牦牛、拉日马牦牛以及其他7个地方牦牛群体(九龙牦牛、麦洼牦牛、金川牦牛、昌台牦牛、中甸牦牛、玉树牦牛、类乌齐牦牛)进行RAD简化基因组测序,基于检测到的SNP信息计算遗传统计量。结果表明,亚丁牦牛和拉日马牦牛的观测杂合度分别为0.2186、0.2233,亚丁牦牛遗传多样性较贫乏。亚丁牦牛的平均遗传分化指数Fst值最高为0.0653,与其他8个牦牛群体存在中度分化,Structure分析显示其血统构成纯正,可列为一个独立遗传资源。拉日马牦牛Fst值最低为0.0443,其群体遗传结构较复杂,与九龙牦牛和麦洼牦牛存在基因交流,属麦洼牦牛的祖先群之一。亚丁牦牛和拉日马牦牛均值得进一步研究和保护,研究结果对牦牛遗传资源的保护与利用具有重要意义。
纪会, 官久强, 王会, 周建旭, 阿农呷, 何宗伟, 樊珍详, 邱龙康, 曹诗晓, 安添午, 柏琴, 钟金城, 罗晓林. 亚丁牦牛和拉日马牦牛遗传多样性及遗传结构分析[J]. 草业学报, 2021, 30(5): 134-145.
Hui JI, Jiu-qiang GUAN, Hui WANG, Jian-xu ZHOU, Nong-ga A, Zong-wei HE, Zhen-xiang FAN, Long-kang QIU, Shi-xiao CAO, Tian-wu AN, Qin BAI, Jin-cheng ZHONG, Xiao-lin LUO. Genetic structure and diversity of Yading yak and Larima yak populations[J]. Acta Prataculturae Sinica, 2021, 30(5): 134-145.
序号Number | 品种Population | 代号Code | 样本量Sample size | 地理位置Geographic position |
---|---|---|---|---|
1 | 亚丁牦牛Yading yak | YD | 10 | 四川稻城县Daocheng County, Sichuan |
2 | 拉日马牦牛Larima yak | LRM | 10 | 四川新龙县Xinlong County, Sichuan |
3 | 九龙牦牛Jiulong yak | JL | 10 | 四川九龙县Jiulong County, Sichuan |
4 | 麦洼牦牛Maiwa yak | MW | 11 | 四川红原县Hongyuan County, Sichuan |
5 | 昌台牦牛Changtai yak | CT | 9 | 四川白玉县Baiyu County, Sichuan |
6 | 金川牦牛Jinchuan yak | JC | 9 | 四川金川县Jinchuan County, Sichuan |
7 | 中甸牦牛Zhongdian yak | ZD | 10 | 云南香格里拉县Shangrila County, Yunnan |
8 | 类乌齐牦牛Leiwuqi yak | LWQ | 9 | 西藏类乌齐县Leiwuqi County, Tibet |
9 | 玉树牦牛Yushu yak | YS | 10 | 青海曲麻莱县Qumalai County, Qinghai |
总计Total | - | - | 88 | - |
表1 牦牛样本来源及样本量
Table 1 Source and number of yak sample
序号Number | 品种Population | 代号Code | 样本量Sample size | 地理位置Geographic position |
---|---|---|---|---|
1 | 亚丁牦牛Yading yak | YD | 10 | 四川稻城县Daocheng County, Sichuan |
2 | 拉日马牦牛Larima yak | LRM | 10 | 四川新龙县Xinlong County, Sichuan |
3 | 九龙牦牛Jiulong yak | JL | 10 | 四川九龙县Jiulong County, Sichuan |
4 | 麦洼牦牛Maiwa yak | MW | 11 | 四川红原县Hongyuan County, Sichuan |
5 | 昌台牦牛Changtai yak | CT | 9 | 四川白玉县Baiyu County, Sichuan |
6 | 金川牦牛Jinchuan yak | JC | 9 | 四川金川县Jinchuan County, Sichuan |
7 | 中甸牦牛Zhongdian yak | ZD | 10 | 云南香格里拉县Shangrila County, Yunnan |
8 | 类乌齐牦牛Leiwuqi yak | LWQ | 9 | 西藏类乌齐县Leiwuqi County, Tibet |
9 | 玉树牦牛Yushu yak | YS | 10 | 青海曲麻莱县Qumalai County, Qinghai |
总计Total | - | - | 88 | - |
群体 Population | 原始数据 Raw data (M) | 有效数据 Valid data (M) | 有效率 Effective rate (%) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|---|
YS | 524.6 | 486.3 | 92.69 | 97.16 | 91.81 | 48.35 |
MW | 513.6 | 466.6 | 90.84 | 97.88 | 93.61 | 48.75 |
ZD | 508.6 | 484.8 | 95.33 | 97.30 | 92.19 | 48.76 |
YD | 484.3 | 435.1 | 89.82 | 96.93 | 91.47 | 48.92 |
LRM | 464.9 | 440.4 | 94.75 | 96.99 | 91.55 | 49.07 |
JC | 455.9 | 427.6 | 93.80 | 97.46 | 92.57 | 48.96 |
LWQ | 433.4 | 403.9 | 93.18 | 97.00 | 91.55 | 48.64 |
JL | 419.2 | 400.5 | 95.54 | 97.22 | 92.03 | 48.92 |
CT | 401.5 | 371.3 | 92.47 | 97.66 | 93.06 | 48.78 |
表2 测序数据质量汇总情况
Table 2 Summary of sequencing data quality
群体 Population | 原始数据 Raw data (M) | 有效数据 Valid data (M) | 有效率 Effective rate (%) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|---|
YS | 524.6 | 486.3 | 92.69 | 97.16 | 91.81 | 48.35 |
MW | 513.6 | 466.6 | 90.84 | 97.88 | 93.61 | 48.75 |
ZD | 508.6 | 484.8 | 95.33 | 97.30 | 92.19 | 48.76 |
YD | 484.3 | 435.1 | 89.82 | 96.93 | 91.47 | 48.92 |
LRM | 464.9 | 440.4 | 94.75 | 96.99 | 91.55 | 49.07 |
JC | 455.9 | 427.6 | 93.80 | 97.46 | 92.57 | 48.96 |
LWQ | 433.4 | 403.9 | 93.18 | 97.00 | 91.55 | 48.64 |
JL | 419.2 | 400.5 | 95.54 | 97.22 | 92.03 | 48.92 |
CT | 401.5 | 371.3 | 92.47 | 97.66 | 93.06 | 48.78 |
群体 Population | 观测杂合度 Observed heterozygosity (Ho) | 期望杂合度 Expected heterozygosity (He) | He-Ho |
---|---|---|---|
YS | 0.2440 | 0.2841 | 0.0401 |
JC | 0.2354 | 0.2798 | 0.0443 |
ZD | 0.2307 | 0.2735 | 0.0428 |
LWQ | 0.2283 | 0.2732 | 0.0449 |
MW | 0.2278 | 0.2803 | 0.0525 |
LRM | 0.2233 | 0.2799 | 0.0566 |
CT | 0.2230 | 0.2782 | 0.0552 |
YD | 0.2186 | 0.2570 | 0.0383 |
JL | 0.2172 | 0.2665 | 0.0493 |
平均值Mean | 0.2276 | 0.2747 | 0.0471 |
表3 9个牦牛群体的杂合度
Table 3 Heterozygosity of 9 yak populations
群体 Population | 观测杂合度 Observed heterozygosity (Ho) | 期望杂合度 Expected heterozygosity (He) | He-Ho |
---|---|---|---|
YS | 0.2440 | 0.2841 | 0.0401 |
JC | 0.2354 | 0.2798 | 0.0443 |
ZD | 0.2307 | 0.2735 | 0.0428 |
LWQ | 0.2283 | 0.2732 | 0.0449 |
MW | 0.2278 | 0.2803 | 0.0525 |
LRM | 0.2233 | 0.2799 | 0.0566 |
CT | 0.2230 | 0.2782 | 0.0552 |
YD | 0.2186 | 0.2570 | 0.0383 |
JL | 0.2172 | 0.2665 | 0.0493 |
平均值Mean | 0.2276 | 0.2747 | 0.0471 |
群体Population | CT | JC | JL | LRM | MW | YD | YS | ZD | 平均值Mean |
---|---|---|---|---|---|---|---|---|---|
LWQ | 0.0465 | 0.0477 | 0.0548 | 0.0444 | 0.0450 | 0.0698 | 0.0432 | 0.0532 | 0.0506 |
CT | 0.0399 | 0.0496 | 0.0394 | 0.0399 | 0.0639 | 0.0396 | 0.0475 | 0.0458 | |
JC | 0.0507 | 0.0408 | 0.0406 | 0.0659 | 0.0404 | 0.0487 | 0.0468 | ||
JL | 0.0459 | 0.0479 | 0.0697 | 0.0479 | 0.0527 | 0.0524 | |||
LRM | 0.0380 | 0.0626 | 0.0379 | 0.0453 | 0.0443 | ||||
MW | 0.0631 | 0.0380 | 0.0464 | 0.0449 | |||||
YD | 0.0639 | 0.0632 | 0.0653 | ||||||
YS | 0.0464 | 0.0447 | |||||||
ZD | 0.0504 |
表4 群体间Pairwise Fst
Table 4 Pairwise Fst between population
群体Population | CT | JC | JL | LRM | MW | YD | YS | ZD | 平均值Mean |
---|---|---|---|---|---|---|---|---|---|
LWQ | 0.0465 | 0.0477 | 0.0548 | 0.0444 | 0.0450 | 0.0698 | 0.0432 | 0.0532 | 0.0506 |
CT | 0.0399 | 0.0496 | 0.0394 | 0.0399 | 0.0639 | 0.0396 | 0.0475 | 0.0458 | |
JC | 0.0507 | 0.0408 | 0.0406 | 0.0659 | 0.0404 | 0.0487 | 0.0468 | ||
JL | 0.0459 | 0.0479 | 0.0697 | 0.0479 | 0.0527 | 0.0524 | |||
LRM | 0.0380 | 0.0626 | 0.0379 | 0.0453 | 0.0443 | ||||
MW | 0.0631 | 0.0380 | 0.0464 | 0.0449 | |||||
YD | 0.0639 | 0.0632 | 0.0653 | ||||||
YS | 0.0464 | 0.0447 | |||||||
ZD | 0.0504 |
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