草业学报 ›› 2022, Vol. 31 ›› Issue (1): 131-144.DOI: 10.11686/cyxb2020481
• 研究论文 • 上一篇
收稿日期:
2020-10-27
修回日期:
2020-12-28
出版日期:
2021-12-01
发布日期:
2021-12-01
通讯作者:
刘文献
作者简介:
Corresponding author. E-mail: liuwx@lzu.edu.cn基金资助:
Xiao-fan YIN(), Na WEI, Shu-wen ZHENG, Wen-xian LIU()
Received:
2020-10-27
Revised:
2020-12-28
Online:
2021-12-01
Published:
2021-12-01
Contact:
Wen-xian LIU
摘要:
由于苜蓿品种间遗传差异日益缩小,通过传统形态学鉴定表型愈加困难。在苜蓿育种过程中,利用分子标记可大大提高育种效率和品种鉴定。反转录转座子长末端重复序列(LTR)广泛分布在植物基因组中,基于LTR的分子标记具有丰富的多态性和高信息量等优势,被广泛用于物种品种鉴定、评价种质资源多样性等方面。本研究在全基因组水平鉴定和设计了大量蒺藜苜蓿LTR反转录转座子扩增多态性(IRAP)标记,并利用其对国内外40个紫花苜蓿种质资源进行遗传多样性分析。结果表明,根据设计开发出的431个IRAP引物,并按照其染色体位置信息组合获得69对IRAP引物。利用筛选出的37对多态性引物组合共扩增出325个等位位点,平均每个标记可产生8.8个等位位点;多态性条带比率(PPB)为50%~100%,平均值为79.9%;多态性信息含量(PIC)的范围为0.34~0.88,平均值为0.69。基于遗传相似系数(GS)对供试品种采用算术平均值非加权组平均法(UPGMA)进行聚类分析,以0.82为阈值可将40份供试材料分为4类,其分组结果与不同材料地理分布信息以及STRUCTURE分析相对一致。本研究首次在蒺藜苜蓿全基因组水平上开发了IRAP分子标记并在紫花苜蓿种质资源中进行评价与应用,获得的大量IRAP分子标记可对后续苜蓿品种的鉴定保护以及遗传背景分析提供技术支撑。
尹晓凡, 魏娜, 郑淑文, 刘文献. 全基因组水平蒺藜苜蓿反转录转座子IRAP分子标记开发及应用[J]. 草业学报, 2022, 31(1): 131-144.
Xiao-fan YIN, Na WEI, Shu-wen ZHENG, Wen-xian LIU. Genome-wide development and utilization of LTR retrotransposon-based IRAP markers in Medicago truncatula[J]. Acta Prataculturae Sinica, 2022, 31(1): 131-144.
编号No. | 标准品种Example varieties | 种属Species | 类型Type | 来源Origins |
---|---|---|---|---|
1 | 中牧1号Zhongmu 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
2 | 中苜1号Zhongmu 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
3 | 中苜2号Zhongmu 2 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
4 | 中兰1号Zhonglan 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
5 | 甘农7号Gannong 7 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
6 | 甘农2号Gannong 2 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
7 | 甘农3号Gannong 3 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
8 | 甘农4号Gannong 4 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
9 | 无棣苜蓿Wudi | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
10 | 新疆大叶Xinjiangdaye | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
11 | 保定苜蓿Baoding | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
12 | 东苜1号Dongmu 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
13 | 公农1号Gongnong 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
14 | 公农2号Gongnong 2 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
15 | 公农3号Gongnong 3 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
16 | 龙牧808 Longmu 808 | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
17 | 天水苜蓿Tianshui | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
18 | 新牧2号Xinmu 2 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
19 | 图牧1号Tumu 1 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
20 | 陇东苜蓿Longdong | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
21 | Abi 700 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
22 | Arc | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
23 | Archer | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
24 | Boja | 紫花苜蓿M. sativa notho. varia | 品种Cultivar | 波兰Poland |
25 | CUF 101 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
26 | Derby | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 英国United Kingdom |
27 | Europe | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 法国France |
28 | Hunter River | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 墨西哥Mexico |
29 | Hunterfield | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 奥地利Austria |
30 | IFMP 798 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 沙特阿拉伯Saudi Arabia |
31 | Aurora | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 危地马拉Guatemala |
32 | IFMP 799 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 沙特阿拉伯Saudi Arabia |
33 | Orca | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 法国France |
34 | Ranger | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
35 | Saranac AR | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
36 | Sutter | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
37 | Trifecta | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 奥地利Austria |
38 | Vernal | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
39 | WL168HQ | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
40 | WL343HQ | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
表1 40份紫花苜蓿种质类型及来源
Table 1 40 alfalfa germplasm types and sources
编号No. | 标准品种Example varieties | 种属Species | 类型Type | 来源Origins |
---|---|---|---|---|
1 | 中牧1号Zhongmu 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
2 | 中苜1号Zhongmu 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
3 | 中苜2号Zhongmu 2 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
4 | 中兰1号Zhonglan 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
5 | 甘农7号Gannong 7 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
6 | 甘农2号Gannong 2 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
7 | 甘农3号Gannong 3 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
8 | 甘农4号Gannong 4 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
9 | 无棣苜蓿Wudi | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
10 | 新疆大叶Xinjiangdaye | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
11 | 保定苜蓿Baoding | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
12 | 东苜1号Dongmu 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
13 | 公农1号Gongnong 1 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
14 | 公农2号Gongnong 2 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
15 | 公农3号Gongnong 3 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
16 | 龙牧808 Longmu 808 | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
17 | 天水苜蓿Tianshui | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
18 | 新牧2号Xinmu 2 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 中国China |
19 | 图牧1号Tumu 1 | 杂花苜蓿M. sativa Martin | 品种Cultivar | 中国China |
20 | 陇东苜蓿Longdong | 紫花苜蓿M. sativa ssp. sativa | 地方种Land race | 中国China |
21 | Abi 700 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
22 | Arc | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
23 | Archer | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
24 | Boja | 紫花苜蓿M. sativa notho. varia | 品种Cultivar | 波兰Poland |
25 | CUF 101 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
26 | Derby | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 英国United Kingdom |
27 | Europe | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 法国France |
28 | Hunter River | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 墨西哥Mexico |
29 | Hunterfield | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 奥地利Austria |
30 | IFMP 798 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 沙特阿拉伯Saudi Arabia |
31 | Aurora | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 危地马拉Guatemala |
32 | IFMP 799 | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 沙特阿拉伯Saudi Arabia |
33 | Orca | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 法国France |
34 | Ranger | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
35 | Saranac AR | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
36 | Sutter | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
37 | Trifecta | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 奥地利Austria |
38 | Vernal | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
39 | WL168HQ | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
40 | WL343HQ | 紫花苜蓿M. sativa ssp. sativa | 品种Cultivar | 美国United States |
引物名称 Primer name | 正向引物 Forward primer (5'-3') | 反向引物 Reverse primer (5'-3') | 退火温度 Annealing temperature (℃) |
---|---|---|---|
C1~C1 | GCACTATACTCACACACTCAC | TCCAGAGCATAATTGTTGAAGC | 52 |
C2~G1 | AGGCAAACACAGGGACTAAAATAG | GGGGCATTTTGGTCTTTTCC | 53 |
C2~C1 | TTCTCCGCTTGTGACATGG | CAACGTGGCACGATGGAG | 53 |
C3~G1 | TGAATGAGGGTGGCTGGTC | GTTTCAAGTGCCAAGGTAAAGG | 54 |
C3~C1 | AATAGCCTTACAAGCAAAACTGAG | CAACCGTCCATTCCTAAATTCG | 53 |
C4~G1 | TTGCTCCTTTGTAACTGCTCAG | TTGGCTCTGAATCCTTGTTACG | 54 |
C4~C1 | GCAAAGCTAACCCTAATTACAC | TTTGGCGGGAAAAGTTTGTTAC | 51 |
C5~G1 | TCATAATGGGCTTGGACCTTAC | AATCCCAATGCCTCCCAAAATC | 53 |
C5~C1 | AAGTTTGGTTAGGTTGCTTGAAG | ACATCAAGAGCCTTTGGTTTCG | 54 |
C6~G1 | TCACAATATGCCTGCCTCTC | TGCTTCCAACATCACCAAATAG | 53 |
C6~C1 | TGTTGAATGCGGATGACTGAAG | CCAATCCGCCAGCAGTTG | 54 |
C7~G1 | GCCACACCTTCTTCAACTTG | GAGAACAAGGTGAACAATTCCAAC | 52 |
C7~C1 | TCCTAAAGACTTGGTCAATCAG | TGTGAGTGAAGTGAGTGAAACC | 51 |
C8~G1 | TCTTGGGCTGGGCTCATC | CTCCACCGCATTCTTCTAAGC | 54 |
C8~C1 | TGGTGTTTCCTTCAGCGTTTC | ACTTCGTTACTTGGTTAGTTAC | 50 |
C1~G2 | GCACTTGAACCATCACACATAG | GGTGCTTTCATTGCTCCTATTC | 53 |
C1~C2 | CTTGATTTCTTGTCTCCTATCG | AGGTGGAATTGTGACTAACTTG | 50 |
C2~G2 | TTCCCAGTCAAATCCTCAGATG | GGAACCGTTGTACCGTTATGG | 53 |
C2~C2 | GGAAAGTAGAAAGGCAAATACG | TCTGTGAGATGAATGCTGAAAC | 51 |
C3~G2 | CCTGAATGTTGAATGTGCCTTC | TTGGTGCTCTCGTTGTCATAAC | 54 |
C3~C2 | CTAGTGGTGAGTGGCAACTG | AAGCAGCAACCTTTGACATTC | 53 |
C4~G2 | CCAGGGAGCCAACAGAGG | GGCTGATAACACTCGTATGAAG | 52 |
C4~C2 | ACGACTGAATGAAATGTGAAAC | AACACCGCAATCCAATACCTAAG | 51 |
C5~C2 | CCTACAACGTGGAATGACTTAG | AGTGTGAGAGAAACAGTGAGTG | 52 |
C6~G2 | ATCATTCATAGAGACGCAGCTC | CCATCAAACCCATCAACCAAAG | 54 |
C6~C2 | CAGCACTGCCACTTCTTG | CAACTCCAACAACGGCTCTC | 51 |
C7~G2 | TATTTGTGATGGATGGCTACTC | GTAATGAGATTGGTGATGAGTC | 50 |
C7~C2 | CACACGTTGCCAATACTTCAG | CAGAGCTATCATCTCACAGGAC | 53 |
C8~G2 | TCCACCAGTAGGCATCTTCATC | ATGTGGTGACTCCCCTAGTTC | 54 |
C8~C2 | TGCCTTGTCAATACATAGAACC | TGGCAACGTCAAATTCAAATTC | 52 |
C1~G3 | CCTAACGGCATACTACAGATGG | GTGCTCTCGTGTTCTGTAACTC | 54 |
C1~C3 | TCACCACATACTGCTTACTTTC | GGCTTCCACAAACAACCCTTC | 52 |
C2~G3 | AAGCAGAAGGGGTGAGATTTC | CGGTCAATTAGAGAGTCGTGTC | 53 |
C3~G3 | TATGGCGGCGATATAATAATGC | CGATCCAAGGAACAACTGAGTC | 52 |
C3~C3 | TTCAGTACTTGGCATATATATAGC | AGTGGTATCAGGAGTCCTTAGG | 50 |
C4~G3 | TGGAGCAGTTCTCTTCCTTTTC | GCTTTCATCTTCACTCACCATG | 53 |
C4~C3 | ACCCTAACTCACGGCATCC | GGGCAACGGTAGTGATTTGG | 54 |
C5~C3 | AGCATATCAGAGAGTTCCTAAC | TGTGAGTGAAGTGAGTGAAACC | 50 |
C6~G3 | GCTTCTTCGATTCCTGCTGAG | CGCCCAGTGGAACCTTTTG | 54 |
C6~C3 | ACCGTGCTCACCAAATCG | TGGGGCAGAGGGTTAAAGG | 53 |
C7~G3 | ATCCAAGATGCCTACTCTCAAC | CGTTGGAGAATCAGTGAATGC | 53 |
C7~C3 | TGCATCAAATCGTTCTTCATAC | GTGGGGCAAGGGTCAAAG | 51 |
C8~G3 | GATTGATGACAGGAAGGTGAAG | ACACCCCGTTACCCAAAAG | 52 |
C8~C3 | TACTGCCTGACTATTTTCATTC | AAACACAAACCTGCTGCAATTC | 50 |
C1~G4 | TCCACAACCACACCCAATAAC | AATCGCAACTTTGGAGGTTTC | 53 |
C1~C4 | TTGTCGTGTACGGTATATTGGG | AGTGGTATCAGAGCGGTCTTC | 54 |
C2~G4 | CTCCCAAACCAAACCCAAAC | GGTCCAAACACTCTCACAAATG | 53 |
C3~G4 | AGCATAAGGACATTAGCCACTC | CTTCCCAATGCCTCCCAAAC | 54 |
C3~C4 | CCACTAGCAGCCTAACTAACC | TATCAGAGCCTCACCACGAG | 53 |
C4~G4 | TAGCGGTGACTTCTCCCATC | TTGGTGCTTTCATTGCCTCTAC | 54 |
C5~C4 | AATCTTCTCCGCCTTCTTCTG | GAACCACCGTCCGCTGAC | 53 |
C6~G4 | CGTCCTTTACTGATGCTGATGG | ACTTGGTGCTTTCATTTCCTTC | 53 |
C7~G4 | CCTATTACAGACTTGGGCCATG | ACTCCATGCCTCCCAAACC | 54 |
C8~G4 | AAACTGACATAAGGCCCAATAC | ATGCCTCCTAAACCTACAAACC | 52 |
C1~G5 | TCGCTGTTCCTGAAGTAGAAG | AATGGGGCGTAGCTTTGTG | 53 |
C1~C5 | ACAGCAGGACAGCATAGTAG | AACCCTTGCTTTCTTGACACC | 52 |
C2~G5 | TTCACCCCTTTTGTCCTTTTCC | AAGATGGGTGACCGTTTAGATG | 54 |
C3~G5 | AGGAAGGCTCTACATTACAAAC | TTGGTATCAGAGCTGGTTACG | 51 |
C4~G5 | AAGGCTCTCCATTACAAACTAG | GTTACGATACCACGGAGTTGAG | 51 |
C6~G5 | TTGCTCCTTCTTGTGGTACTTC | AACCCAAACACCGACACTTG | 54 |
C1~C6 | TGGTGGGATTGTTTGGAAGTAC | TGCTTAGGACTGCTGATGTG | 53 |
C2~G6 | TCTGGGCTTTATTTGGTGGATC | GGTGCTTTCATTGCCATCCTG | 54 |
C3~G6 | GCCACGTCATGCTTCTTTC | GTAGATGCCACCAAAGCCTAAG | 52 |
C4~G6 | GACAACACTGCTAAGACAACAC | GCCAAGTAGTAGAGTCGTGTTG | 54 |
C6~G6 | ACCCTAAGGATGAAAGAAAACG | ACCATGATGCCACGAAACC | 52 |
C2~G7 | GCCTGGACTTGTTTCTCTTAGC | ACTCACAACGATGCCTTACAAG | 55 |
C3~G7 | CATCGTTTCTTCCAGCCATTTC | AATTATTGGATACACGACTACG | 50 |
C6~G7 | TGGAGGCGGATAGGGTTTC | AGGAGGATATTGGACACTATGG | 52 |
C3~G8 | AACAAGCCAGTACAATGAACAG | GGAATTGACCACCGAGTTACG | 53 |
表2 引物信息及序列
Table 2 Primer and sequences information applied in this study
引物名称 Primer name | 正向引物 Forward primer (5'-3') | 反向引物 Reverse primer (5'-3') | 退火温度 Annealing temperature (℃) |
---|---|---|---|
C1~C1 | GCACTATACTCACACACTCAC | TCCAGAGCATAATTGTTGAAGC | 52 |
C2~G1 | AGGCAAACACAGGGACTAAAATAG | GGGGCATTTTGGTCTTTTCC | 53 |
C2~C1 | TTCTCCGCTTGTGACATGG | CAACGTGGCACGATGGAG | 53 |
C3~G1 | TGAATGAGGGTGGCTGGTC | GTTTCAAGTGCCAAGGTAAAGG | 54 |
C3~C1 | AATAGCCTTACAAGCAAAACTGAG | CAACCGTCCATTCCTAAATTCG | 53 |
C4~G1 | TTGCTCCTTTGTAACTGCTCAG | TTGGCTCTGAATCCTTGTTACG | 54 |
C4~C1 | GCAAAGCTAACCCTAATTACAC | TTTGGCGGGAAAAGTTTGTTAC | 51 |
C5~G1 | TCATAATGGGCTTGGACCTTAC | AATCCCAATGCCTCCCAAAATC | 53 |
C5~C1 | AAGTTTGGTTAGGTTGCTTGAAG | ACATCAAGAGCCTTTGGTTTCG | 54 |
C6~G1 | TCACAATATGCCTGCCTCTC | TGCTTCCAACATCACCAAATAG | 53 |
C6~C1 | TGTTGAATGCGGATGACTGAAG | CCAATCCGCCAGCAGTTG | 54 |
C7~G1 | GCCACACCTTCTTCAACTTG | GAGAACAAGGTGAACAATTCCAAC | 52 |
C7~C1 | TCCTAAAGACTTGGTCAATCAG | TGTGAGTGAAGTGAGTGAAACC | 51 |
C8~G1 | TCTTGGGCTGGGCTCATC | CTCCACCGCATTCTTCTAAGC | 54 |
C8~C1 | TGGTGTTTCCTTCAGCGTTTC | ACTTCGTTACTTGGTTAGTTAC | 50 |
C1~G2 | GCACTTGAACCATCACACATAG | GGTGCTTTCATTGCTCCTATTC | 53 |
C1~C2 | CTTGATTTCTTGTCTCCTATCG | AGGTGGAATTGTGACTAACTTG | 50 |
C2~G2 | TTCCCAGTCAAATCCTCAGATG | GGAACCGTTGTACCGTTATGG | 53 |
C2~C2 | GGAAAGTAGAAAGGCAAATACG | TCTGTGAGATGAATGCTGAAAC | 51 |
C3~G2 | CCTGAATGTTGAATGTGCCTTC | TTGGTGCTCTCGTTGTCATAAC | 54 |
C3~C2 | CTAGTGGTGAGTGGCAACTG | AAGCAGCAACCTTTGACATTC | 53 |
C4~G2 | CCAGGGAGCCAACAGAGG | GGCTGATAACACTCGTATGAAG | 52 |
C4~C2 | ACGACTGAATGAAATGTGAAAC | AACACCGCAATCCAATACCTAAG | 51 |
C5~C2 | CCTACAACGTGGAATGACTTAG | AGTGTGAGAGAAACAGTGAGTG | 52 |
C6~G2 | ATCATTCATAGAGACGCAGCTC | CCATCAAACCCATCAACCAAAG | 54 |
C6~C2 | CAGCACTGCCACTTCTTG | CAACTCCAACAACGGCTCTC | 51 |
C7~G2 | TATTTGTGATGGATGGCTACTC | GTAATGAGATTGGTGATGAGTC | 50 |
C7~C2 | CACACGTTGCCAATACTTCAG | CAGAGCTATCATCTCACAGGAC | 53 |
C8~G2 | TCCACCAGTAGGCATCTTCATC | ATGTGGTGACTCCCCTAGTTC | 54 |
C8~C2 | TGCCTTGTCAATACATAGAACC | TGGCAACGTCAAATTCAAATTC | 52 |
C1~G3 | CCTAACGGCATACTACAGATGG | GTGCTCTCGTGTTCTGTAACTC | 54 |
C1~C3 | TCACCACATACTGCTTACTTTC | GGCTTCCACAAACAACCCTTC | 52 |
C2~G3 | AAGCAGAAGGGGTGAGATTTC | CGGTCAATTAGAGAGTCGTGTC | 53 |
C3~G3 | TATGGCGGCGATATAATAATGC | CGATCCAAGGAACAACTGAGTC | 52 |
C3~C3 | TTCAGTACTTGGCATATATATAGC | AGTGGTATCAGGAGTCCTTAGG | 50 |
C4~G3 | TGGAGCAGTTCTCTTCCTTTTC | GCTTTCATCTTCACTCACCATG | 53 |
C4~C3 | ACCCTAACTCACGGCATCC | GGGCAACGGTAGTGATTTGG | 54 |
C5~C3 | AGCATATCAGAGAGTTCCTAAC | TGTGAGTGAAGTGAGTGAAACC | 50 |
C6~G3 | GCTTCTTCGATTCCTGCTGAG | CGCCCAGTGGAACCTTTTG | 54 |
C6~C3 | ACCGTGCTCACCAAATCG | TGGGGCAGAGGGTTAAAGG | 53 |
C7~G3 | ATCCAAGATGCCTACTCTCAAC | CGTTGGAGAATCAGTGAATGC | 53 |
C7~C3 | TGCATCAAATCGTTCTTCATAC | GTGGGGCAAGGGTCAAAG | 51 |
C8~G3 | GATTGATGACAGGAAGGTGAAG | ACACCCCGTTACCCAAAAG | 52 |
C8~C3 | TACTGCCTGACTATTTTCATTC | AAACACAAACCTGCTGCAATTC | 50 |
C1~G4 | TCCACAACCACACCCAATAAC | AATCGCAACTTTGGAGGTTTC | 53 |
C1~C4 | TTGTCGTGTACGGTATATTGGG | AGTGGTATCAGAGCGGTCTTC | 54 |
C2~G4 | CTCCCAAACCAAACCCAAAC | GGTCCAAACACTCTCACAAATG | 53 |
C3~G4 | AGCATAAGGACATTAGCCACTC | CTTCCCAATGCCTCCCAAAC | 54 |
C3~C4 | CCACTAGCAGCCTAACTAACC | TATCAGAGCCTCACCACGAG | 53 |
C4~G4 | TAGCGGTGACTTCTCCCATC | TTGGTGCTTTCATTGCCTCTAC | 54 |
C5~C4 | AATCTTCTCCGCCTTCTTCTG | GAACCACCGTCCGCTGAC | 53 |
C6~G4 | CGTCCTTTACTGATGCTGATGG | ACTTGGTGCTTTCATTTCCTTC | 53 |
C7~G4 | CCTATTACAGACTTGGGCCATG | ACTCCATGCCTCCCAAACC | 54 |
C8~G4 | AAACTGACATAAGGCCCAATAC | ATGCCTCCTAAACCTACAAACC | 52 |
C1~G5 | TCGCTGTTCCTGAAGTAGAAG | AATGGGGCGTAGCTTTGTG | 53 |
C1~C5 | ACAGCAGGACAGCATAGTAG | AACCCTTGCTTTCTTGACACC | 52 |
C2~G5 | TTCACCCCTTTTGTCCTTTTCC | AAGATGGGTGACCGTTTAGATG | 54 |
C3~G5 | AGGAAGGCTCTACATTACAAAC | TTGGTATCAGAGCTGGTTACG | 51 |
C4~G5 | AAGGCTCTCCATTACAAACTAG | GTTACGATACCACGGAGTTGAG | 51 |
C6~G5 | TTGCTCCTTCTTGTGGTACTTC | AACCCAAACACCGACACTTG | 54 |
C1~C6 | TGGTGGGATTGTTTGGAAGTAC | TGCTTAGGACTGCTGATGTG | 53 |
C2~G6 | TCTGGGCTTTATTTGGTGGATC | GGTGCTTTCATTGCCATCCTG | 54 |
C3~G6 | GCCACGTCATGCTTCTTTC | GTAGATGCCACCAAAGCCTAAG | 52 |
C4~G6 | GACAACACTGCTAAGACAACAC | GCCAAGTAGTAGAGTCGTGTTG | 54 |
C6~G6 | ACCCTAAGGATGAAAGAAAACG | ACCATGATGCCACGAAACC | 52 |
C2~G7 | GCCTGGACTTGTTTCTCTTAGC | ACTCACAACGATGCCTTACAAG | 55 |
C3~G7 | CATCGTTTCTTCCAGCCATTTC | AATTATTGGATACACGACTACG | 50 |
C6~G7 | TGGAGGCGGATAGGGTTTC | AGGAGGATATTGGACACTATGG | 52 |
C3~G8 | AACAAGCCAGTACAATGAACAG | GGAATTGACCACCGAGTTACG | 53 |
检索项目Search items | Gypsy家族Gypsy family | Copia家族Copia family | 未知Unknown |
---|---|---|---|
已识别的LTR总数Total number of identified LTRs (No.) | 105 | 96 | 230 |
检索序列的总长度Total length of sequences searched (bp) | 265~14644 | 113~10167 | 113~10330 |
检索序列的平均总长度Average total length of the search sequence (bp) | 2837.1 | 2305.5 | 2623.5 |
配对评分的平均值Average of pair rating (%) | 78.7 | 74.4 | 75.2 |
LTR总数的百分比Percentage of total LTRs (%) | 24.40 | 22.30 | 53.40 |
表3 基于蒺藜苜蓿全基因组序列设计引物分类信息
Table 3 Information of designing primers based on the M. truncatula sequence
检索项目Search items | Gypsy家族Gypsy family | Copia家族Copia family | 未知Unknown |
---|---|---|---|
已识别的LTR总数Total number of identified LTRs (No.) | 105 | 96 | 230 |
检索序列的总长度Total length of sequences searched (bp) | 265~14644 | 113~10167 | 113~10330 |
检索序列的平均总长度Average total length of the search sequence (bp) | 2837.1 | 2305.5 | 2623.5 |
配对评分的平均值Average of pair rating (%) | 78.7 | 74.4 | 75.2 |
LTR总数的百分比Percentage of total LTRs (%) | 24.40 | 22.30 | 53.40 |
引物组合 Primer combination | 总条带数 TB (No.) | 多态性条带 PB (No.) | 多态性条带比率 PPB (%) | 预期杂合度 He | 多态性信息含量 PIC |
---|---|---|---|---|---|
C1~C2 | 10 | 7 | 70.0 | 0.82 | 0.79 |
C1~G2 | 12 | 7 | 58.3 | 0.87 | 0.86 |
C2~C1 | 17 | 16 | 94.1 | 0.83 | 0.81 |
C2~C2 | 12 | 11 | 91.7 | 0.84 | 0.82 |
C2~G1 | 4 | 3 | 75.0 | 0.56 | 0.49 |
C2~G2 | 6 | 4 | 66.7 | 0.68 | 0.62 |
C3~C2 | 10 | 9 | 90.0 | 0.72 | 0.68 |
C3~G2 | 5 | 4 | 80.0 | 0.71 | 0.66 |
C4~G1 | 6 | 5 | 83.3 | 0.76 | 0.72 |
C5~C1 | 6 | 5 | 83.3 | 0.61 | 0.57 |
C5~G1 | 13 | 12 | 92.3 | 0.89 | 0.88 |
C6~C1 | 13 | 11 | 84.6 | 0.82 | 0.80 |
C7~G1 | 5 | 4 | 80.0 | 0.55 | 0.45 |
C8~G1 | 5 | 4 | 80.0 | 0.73 | 0.68 |
C8~C1 | 3 | 2 | 66.7 | 0.39 | 0.34 |
C4~G2 | 11 | 9 | 81.8 | 0.80 | 0.77 |
C4~C2 | 7 | 5 | 71.4 | 0.69 | 0.64 |
C5~C2 | 7 | 5 | 71.4 | 0.80 | 0.77 |
C6~G2 | 10 | 7 | 70.0 | 0.82 | 0.79 |
C6~C2 | 15 | 12 | 80.0 | 0.83 | 0.81 |
C7~C2 | 16 | 15 | 93.8 | 0.89 | 0.88 |
C8~G2 | 8 | 8 | 100.0 | 0.74 | 0.69 |
C8~C2 | 3 | 2 | 66.7 | 0.48 | 0.39 |
C1~G3 | 17 | 16 | 94.1 | 0.87 | 0.86 |
C1~C3 | 9 | 8 | 88.9 | 0.85 | 0.83 |
C3~G3 | 11 | 9 | 81.8 | 0.86 | 0.84 |
C6~C3 | 6 | 4 | 66.7 | 0.71 | 0.66 |
C7~G3 | 7 | 4 | 57.1 | 0.75 | 0.71 |
C2~G4 | 6 | 5 | 83.3 | 0.47 | 0.43 |
C3~G4 | 4 | 2 | 50.0 | 0.62 | 0.54 |
C6~G4 | 4 | 3 | 75.0 | 0.67 | 0.60 |
C7~G4 | 9 | 7 | 77.8 | 0.84 | 0.82 |
C8~G4 | 7 | 5 | 71.4 | 0.71 | 0.65 |
C2~G5 | 13 | 11 | 84.6 | 0.85 | 0.83 |
C4~G5 | 15 | 14 | 93.3 | 0.85 | 0.83 |
C5~C4 | 9 | 9 | 100.0 | 0.53 | 0.51 |
C1~G5 | 4 | 4 | 100.0 | 0.69 | 0.63 |
总数Total | 325 | 268 | 82.5 | - | - |
平均值Average | 8.8 | 7.2 | 79.9 | 0.73 | 0.69 |
表4 37对多态性IRAP标记引物信息
Table 4 Information of 37 pairs of polymorphic IRAP marker primers
引物组合 Primer combination | 总条带数 TB (No.) | 多态性条带 PB (No.) | 多态性条带比率 PPB (%) | 预期杂合度 He | 多态性信息含量 PIC |
---|---|---|---|---|---|
C1~C2 | 10 | 7 | 70.0 | 0.82 | 0.79 |
C1~G2 | 12 | 7 | 58.3 | 0.87 | 0.86 |
C2~C1 | 17 | 16 | 94.1 | 0.83 | 0.81 |
C2~C2 | 12 | 11 | 91.7 | 0.84 | 0.82 |
C2~G1 | 4 | 3 | 75.0 | 0.56 | 0.49 |
C2~G2 | 6 | 4 | 66.7 | 0.68 | 0.62 |
C3~C2 | 10 | 9 | 90.0 | 0.72 | 0.68 |
C3~G2 | 5 | 4 | 80.0 | 0.71 | 0.66 |
C4~G1 | 6 | 5 | 83.3 | 0.76 | 0.72 |
C5~C1 | 6 | 5 | 83.3 | 0.61 | 0.57 |
C5~G1 | 13 | 12 | 92.3 | 0.89 | 0.88 |
C6~C1 | 13 | 11 | 84.6 | 0.82 | 0.80 |
C7~G1 | 5 | 4 | 80.0 | 0.55 | 0.45 |
C8~G1 | 5 | 4 | 80.0 | 0.73 | 0.68 |
C8~C1 | 3 | 2 | 66.7 | 0.39 | 0.34 |
C4~G2 | 11 | 9 | 81.8 | 0.80 | 0.77 |
C4~C2 | 7 | 5 | 71.4 | 0.69 | 0.64 |
C5~C2 | 7 | 5 | 71.4 | 0.80 | 0.77 |
C6~G2 | 10 | 7 | 70.0 | 0.82 | 0.79 |
C6~C2 | 15 | 12 | 80.0 | 0.83 | 0.81 |
C7~C2 | 16 | 15 | 93.8 | 0.89 | 0.88 |
C8~G2 | 8 | 8 | 100.0 | 0.74 | 0.69 |
C8~C2 | 3 | 2 | 66.7 | 0.48 | 0.39 |
C1~G3 | 17 | 16 | 94.1 | 0.87 | 0.86 |
C1~C3 | 9 | 8 | 88.9 | 0.85 | 0.83 |
C3~G3 | 11 | 9 | 81.8 | 0.86 | 0.84 |
C6~C3 | 6 | 4 | 66.7 | 0.71 | 0.66 |
C7~G3 | 7 | 4 | 57.1 | 0.75 | 0.71 |
C2~G4 | 6 | 5 | 83.3 | 0.47 | 0.43 |
C3~G4 | 4 | 2 | 50.0 | 0.62 | 0.54 |
C6~G4 | 4 | 3 | 75.0 | 0.67 | 0.60 |
C7~G4 | 9 | 7 | 77.8 | 0.84 | 0.82 |
C8~G4 | 7 | 5 | 71.4 | 0.71 | 0.65 |
C2~G5 | 13 | 11 | 84.6 | 0.85 | 0.83 |
C4~G5 | 15 | 14 | 93.3 | 0.85 | 0.83 |
C5~C4 | 9 | 9 | 100.0 | 0.53 | 0.51 |
C1~G5 | 4 | 4 | 100.0 | 0.69 | 0.63 |
总数Total | 325 | 268 | 82.5 | - | - |
平均值Average | 8.8 | 7.2 | 79.9 | 0.73 | 0.69 |
图2 部分IRAP引物在编号1~40的苜蓿品种中扩增结果M: 分子量标准标记DNA marker; A: C3~G2; B: C4~G5; C: C6~C1.
Fig. 2 IRAP amplification results of alfalfa varieties coded from 1 to 40 with part of primers
图3 IRAP引物扩增结果相关性分析X1~X37表示引物 C1~C2到C1~G5。X1-X37 indicated the primer ID from C1-C2 to C1-G5.
Fig.3 The correlation analysis based on the IRAP productions
图5 苜蓿IRAP标记STRUCTURE分析A:估计可能的集群(K)的ln P(K)从1到11;B:根据连续K之间ln P(K)的变化率得出ΔK;C:Evanno表输出结果;SD:标准差;D:基于K=3的种群结构。A: Estimated ln P(K) of possible clusters (K) from 1 to 11; B: ΔK based on the rate of change of ln P(K) between successive K; C: Evanno table output results; SD=standard deviation; D: Population structure based on K=3.
Fig.5 STRUCTURE analysis of IRAP markers in alfalfa
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