Acta Prataculturae Sinica ›› 2021, Vol. 30 ›› Issue (5): 134-145.DOI: 10.11686/cyxb2020212
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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
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 | - |
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 |
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 |
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 |
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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