Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (14): 2629-2642.doi: 10.3864/j.issn.0578-1752.2023.14.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Population Genetic Analysis of Puccinia striiformis tritici in Main Winter-Increasing Areas Based on Virulent Phenotypes and Genotypes

GAO XinPei(), ZHAO Jun(), LIU BoFan, GUO Yi, KANG ZhenSheng(), ZHAN GangMing()   

  1. College of Plant Protection, Northwest A & F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, Shaanxi
  • Received:2023-02-27 Accepted:2023-04-11 Online:2023-07-16 Published:2023-07-21
  • Contact: KANG ZhenSheng, ZHAN GangMing

Abstract:

【Objective】To clarify the virulence structure and genetic diversity of Pst populations in the major winter-increasing areas of China, and to provide reference for the prevention and control of Pst and the rational layout of wheat resistance genes in the winter-increasing areas and the wheat production in Huang-huai-hai. 【Method】A total of 148 Pst isolates were collected and isolated from the major winter-increasing areas such as Sichuan Basin, Hubei and southern Henan, and the virulence phenotype was identified by using Chinese differentials and single-gene lines, and 17 pairs of KASP-SNP primers were used to mark the isolates and complete the genotype analysis. 【Result】Based on the Chinese differentials, 14 known races and 63 unknown pathotypes were identified, among which CYR34 (16.2%), G22-14 (12.2%), CYR32 (6.8%), CYR33 (5.4%) were the dominant races (pathotypes); based on the single-gene lines, 113 races (pathotypes) were identified, among which race1 (7.4%), race2 (3.4%), race3 (3.4%) were the dominant races (pathotypes). The Guinong 22 group was the largest epidemic group of Pst population in China’s winter-increasing area, and all tested Pst isolates did not infect single-gene lines varieties carrying Yr5 and Yr15. The virulence phenotype and genotype of CYR34 and G22-14 showed diversification by single-gene lines virulence identification and molecular marker, indicating that there was high differentiation within these two dominant races. The clustering based on the virulence data of two sets of differentials showed that the Pst populations in Sichuan Basin and southern Hubei were similar, while the Pst populations in northwestern Hubei and southern Henan were similar; the genetic clustering based on KASP-SNP molecular data showed that there was genotype differentiation between the Pst populations in Sichuan Basin, southern Hubei and northwestern Hubei, southern Henan; Structure analysis showed that Sichuan Basin, southern Hubei population mainly had two genetic backgrounds, northwestern Hubei, southern Henan population mainly had one genetic background; population genetic differentiation analysis showed that Sichuan Basin Pst population and southern Henan Pst population had the largest Fst value, which was 0.118, with the largest genetic difference and obvious genetic differentiation; northwestern Hubei population and southern Henan population had the smallest degree of genetic differentiation, Fst value was 0.010; gene flow analysis obtained Nm value between northwestern Hubei population and southern Henan population was 25.236, Nm>4, there was a high-level gene flow between them, northwestern Hubei and southern Henan population and Sichuan Basin population had Nm values of 2.923 and 1.864 respectively, both had a low-level gene flow; genetic diversity analysis results showed that Sichuan Basin, southern Hubei region Pst population had a high-level of genetic diversity, northwestern Hubei, southern Henan Pst population had a low-level of genetic diversity. The above conclusions all support that Sichuan Basin, southern Hubei population has genetic differentiation with northwestern Hubei, southern Henan population. 【Conclusion】Single-gene lines can accurately identify Chinese Pst races; Pst populations in China’s major winter-increasing areas have different sources.

Key words: wheat stripe rust, winter-increasing area, virulence identification, KASP-SNP

Table 1

Sampling information in the winter-increasing areas in 2020"

地点
Location
经纬度
Latitude and longitude
海拔
Elevation (m)
样本数
No. of isolate
四川省绵阳市安州区黄土村
Huangtu Village, Anzhou District, Mianyang City, Sichuan Province
104°87′37.72″E,31°78′74.90″N 500 11
四川省绵阳市梓潼县柴坝村
Chaiba Village, Zitong County, Mianyang City, Sichuan Province
105°14′87.27″E,31°58′72.00″N 480 11
四川省绵阳市游仙区新桥镇
Xinqiao Town, Youxian District, Mianyang City, Sichuan Province
104°81′22.71″E,31°55′41.80″N 482 40
四川省泸州市古蔺县丹桂镇
Dangui Town, Gulin County, Luzhou City, Sichuan Province
106°24′11.42″E,27°93′17.21″N 716 19
湖北省荆州市江陵县普济镇
Puji Town, Jiangling County, Jingzhou City, Hubei Province
112°54′15.12″E,29°97′78.52″N 29 19
湖北省随州市曾都区何店镇
Hedian Town, Zengdu District, Suizhou City, Hubei Province
113°33′22.60″E,31°59′22.01″N 77 4
湖北省随州市曾都区万店镇
Wandian Town, Zengdu District, Suizhou City, Hubei Province
113°50′17.24″E,31°83′14.21″N 93 3
湖北省襄阳市枣阳市兴隆镇
Xinglong Town, Zaoyang City, Xiangyang City, Hubei Province
112°90′71.50″E,32°04′67.11″N 157 2
湖北省襄阳市宜城市板桥店镇
Banqiao Dian Town, Yicheng City, Xiangyang City, Hubei Province
112°51′66.40″E,32°31′74.71″N 59 12
湖北省襄阳市襄州区黄集镇
Huangji Town, Xiangzhou District, Xiangyang City, Hubei Province
112°14′03.88″E,32°30′88.91″N 101 5
湖北省鄂州市华容区华容镇
Huarong Town, Huarong District, Ezhou City, Hubei Province
114°73′65.19″E,30°53′50.51″N 37 6
河南省南阳市淅川县厚坡镇
Houpo Town, Xichuan County, Nanyang City, Henan Province
111°76′79.90″E,32°60′77.39″N 147 16

Table 2

Seventeen pairs of KASP-SNP primer sequences with polymorphism"

SNP ID CY32
Contig
CY32_PosIn 正向引物Forward primer (5′-3′) 反向引物
Reverse primer (5′-3′)
正向引物-1 Forward primer-1 正向引物-2 Forward primer-2
KASP1 1 75964 GTGGCTCCTGGTGTAAGTTCC GTGGCTCCTGGTGTAAGTTCT GTGGCCCAAACTACGCTAATTTA
KASP24 4 43862 GGCTTTTCCATTTAGGTCCTTT GGCTTTTCCATTTAGGTCCTTC TGAGGCTGATTGAATTGTGCTT
KASP93 13 397712 ATATCCTGAAAGAACTTGAGTGATTG ATATCCTGAAAGAACTTGAGTGATTT AGGCTTGGTTCGCTATACTCG
KASP150 23 3805 TGTTGATTTTATTTTACAGAGCGATT TGTTGATTTTATTTTACAGAGCGATC CACCTTAAGAAAATTGCGGGA
KASP153 23 3805 TGTTGATTTTATTTTACAGAGCGATT TGTTGATTTTATTTTACAGAGCGATC CACCTTAAGAAAATTGCGGGA
KASP157 24 223357 TGTACTAGTTGGCTTCTCAAGTTCTATT TGTACTAGTTGGCTTCTCAAGTTCTATC ATCACAGAACCTCCAGAGTGAAAT
KASP159 24 654444 CTTTGAATTTGAGGTGATGGCA CTTTGAATTTGAGGTGATGGCG CACGACTTCTGACTAGAACTGCTTG
KASP162 25 232930 AACCAGCCCTGCTCATTGAAATA AACCAGCCCTGCTCATTGAAATC CAGTGGATGTGATGCGTGAGGT
KASP167 26 419659 AAGGTAGGTCGGATATATTTGTCATCT AAGGTAGGTCGGATATATTTGTCATCC CCACTCATGGGCGAAGTTTT
KASP172 27 561290 ATCAAAACAAAGAACCCATCCCA ATCAAAACAAAGAACCCATCCCG CTGAATGTGATTGATTGCCAGGA
KASP177 28 702014 ACAAATTGTCCAACTGGAAAATCA ACAAATTGTCCAACTGGAAAATCG GCCAATCGGTGTCCTTTACG
KASP203 34 225219 CATTGTGACTATCAAGAAAGGATTGT CATTGTGACTATCAAGAAAGGATTGC GGAACCATCCGTCTAAACCC
KASP261 49 33389 TGAGGAGTACTTTCGATAGAATCAGG TGAGGAGTACTTTCGATAGAATCAGA GCCAGCATTCTCCCTCTTACAC
KASP285 56 96991 TAGTTCGTCGATTCCCAAGTTTG TAGTTCGTCGATTCCCAAGTTTA GATGCCGTCGTGATTGTTGC
KASP373 93 6570 CTGTTTGTCAATCGGACCAGC CTGTTTGTCAATCGGACCAGT TGAATAATTCGGTGAAGAGTTTAGTG
KASP392 108 154635 ATTCCACCCACATCAAGACCA ATTCCACCCACATCAAGACCG TACCCTCAGTCAAGTTCATCTATCTACC
KASP436 scaffold314 50233 TTCGTGGGTTACGGTGAGCTT TTCGTGGGTTACGGTGAGCTC AGTGGCACAGTCACCCCTCATA

Table 3

Physiological race identification result"

毒性类群
Group
小种
Race
数量
Number
毒性频率
Frequency (%)
总毒性频率
Total frequency (%)
贵农22类群
Guinong 22 group
CYR34 24 16.2 40.0
G22-14 18 12.2
G22-13 2 1.4
未知Unknown 15 10.1
杂种46类群
Hybrid 46 group
CYR32 10 6.8 29.7
HY-21 3 2.0
HY-8 2 1.4
HY-30 2 1.4
CYR31 1 0.7
未知Unknown 26 17.6
水源11类群
Suwon 11 group
CYR33 8 5.4 18.9
水11-41 Shui 11-41 1 0.7
未知Unknown 19 12.8
洛夫林13类群
Lovrin 13 group
洛13-2 Luo 13-2 4 2.7 8.8
洛13-8 Luo 13-8 3 2.0
洛13-3 Luo 13-3 2 1.4
未知Unknown 4 2.7
其他
Other
CYR24 2 1.4 2.7
未知Unknown 2 1.4

Table 4

The top three physiological races in each region (%)"

地区
Region
四川盆地
Sichuan Basin
湖北南部
Southern Hubei
湖北西北部
Northwestern Hubei
河南南部
Southern Henan
1 CYR34(9.9) CYR34(28.1) CYR34(20.0) CYR34(18.8)
2 G22-14(9.9) G22-14(12.5) G22-14(15.6) G22-14(18.8)
3 CYR32(4.9) CYR32(12.5) CYR33(11.1) G22-13(12.5)

Fig. 1

Virulence frequency of Pst on Chinese differentials SCB: Sichuan basin; S-HB: Southern Hubei; NW-HB: Northwest Hubei; S-HN: South of Henan. The same as below"

Fig. 2

Virulence frequency of Pst on Yr single-gene differentials"

Fig. 3

Cluster analysis of wheat stripe rust population in different regions of winter-increasing area A: Cluster analysis of virulence based on Chinese differentials; B: Cluster analysis of virulence based on Yr single-gene differentials; C: Cluster analysis based on SNP markers"

Fig. 4

Structure analysis of Pst populations in different regions"

Fig. 5

CYR34 and G22-14 cluster analysis of virulence based on Yr single-gene differentials A: CYR34 cluster analysis of virulence based on Yr single-gene differentials; B: G22-14 cluster analysis of virulence based on Yr single-gene differentials"

Fig. 6

Individual cluster analysis of CYR34 and G22-14"

Table 5

Divergence of geographically spaced Pst populations from four regions in term of Fst (upper diagonal) and Nm (lower diagonal)"

地区 Region 四川盆地 SCB 湖北南部 S-HB 湖北西北部 NW-HB 河南南部 S-HN
SCB 0.019 0.079 0.118
S-HB 13.123 0.036 0.036
NW-HB 2.923 6.631 0.010
S-HN 1.864 6.738 25.236

Table 6

Genetic diversity of Pst in different regions"

地区Region Na Ne I Hs NP P (%)
SCB 2.000 1.724 0.591 0.406 17 100.0
S-HB 2.000 1.709 0.584 0.400 17 100.0
NW-HB 1.647 1.523 0.396 0.277 11 64.7
S-HN 1.647 1.557 0.407 0.288 11 64.7

Fig. 7

Indices of multilocus linkage disequilibrium (${{\bar{r}}_{\text{d}}}$) with 1000 replications based on the SNP data"

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