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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (12): 1832-1840.doi: 10.3724/SP.J.1006.2019.91026

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

QTL mapping of adult-plant resistance to stripe rust in wheat variety holdfast

Fang-Ping YANG1,2,Jin-Dong LIU2,3,Ying GUO1,Ao-Lin JIA2,Wei-E WEN2,Kai-Xiang CHAO4,Ling WU5,Wei-Yun YUE6,Ya-Chao DONG2,Xian-Chun XIA2,*()   

  1. 1 Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, Gansu, China
    2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences / National Wheat Improvement Center, Beijing 100081, China
    3 Institute of Shenzhen Agricultural Genome, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong, China
    4 College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China;
    5 Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China
    6 Tianshui Institute of Agricultural Sciences, Tianshui 741200, Gansu, China
  • Received:2019-04-02 Accepted:2019-06-24 Online:2019-12-12 Published:2019-07-19
  • Contact: Xian-Chun XIA E-mail:xiaxianchun@caas.cn
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31360336);the Program of Science and Technology of Lanzhou(2019-1-81);the Youth Fund of Gansu Academy of Agricultural Sciences(2019GAAS41)

Abstract:

Holdfast is an elite wheat cultivar from the United Kingdom with well durable resistance to stripe rust for many years. The aim of the present study was to identify adult-plant resistance (APR) genes to stripe rust in Holdfast and closely linked molecular markers to provide materials and methods for breeding wheat cultivars with durable resistance. A recombinant inbred lines (RIL) population, generated from the cross between Mingxian 169 (highly susceptible) and Holdfast, was planted in Zhongliang and Gangu of Gansu province, and Chengdu of Sichuan province during 2014-2015 and 2015-2016 cropping seasons for evaluating maximum disease severities (MDS) of stripe rust. The chromosomal locations of QTL were firstly determined based on the wheat 660K SNP array and bulked segregant analysis. Then kompetitive allele specific PCR (KASP) markers were developed to genotype the entire RIL population. Finally, the quantitative trait loci (QTLs) mapping of adult-plant resistance to stripe rust in the RIL population were performed, and two QTLs for APR to stripe rust were mapped on chromosomes 5AL and 7AL, respectively. The QTL on chromosome 5AL, designated QYr.gaas-5AL, was identified in all environments, including Zhongliang 2015, Chengdu 2015, Chengdu 2016, Gangu 2015, Gangu 2016, explaining phenotypic variances ranging from 6.5% to 9.3%. QYr.gaas-5AL was flanked by markers Ax-109948955 and Ax-108798241 with genetic distances of 0.5 cM and 1.1 cM, respectively. The 7AL QTL, designated QYr.gaas-7AL, was detected in two environments Gangu 2015 and Gangu 2016, explaining 6.2% and 7.3% of the phenotypic variances, respectively. QYr.gaas-7AL was mapped between markers Ax-110361069 and Ax-108759561 with genetic distances of 0.5 cM and 0.7 cM, respectively. The RILs containing the resistance allele at QYr.gaas-5AL and QYr.gaas-7AL loci were more resistant to stripe rust and had significantly lower MDS than those without the resistance alleles of QYr.gaas-5AL and QYr.gaas-7AL, indicating that QYr.gaas-5AL and QYr.gaas-7Al can effectively reduce stripe rust severities, thus may be used in wheat breeding for improvement of stripe rust resistance.

Key words: common wheat, stripe rust, adult-plant resistance, SNP markers, linkage analysis

Table 1

Correlation coefficients of MDS of stripe rust among different environments"

环境
Environment
中梁2015
Zhongliang 2015
成都2015
Chengdu 2015
甘谷2015
Gangu 2015
成都2016
Chengdu 2016
成都2015 Chengdu 2015 0.40**
甘谷2015 Gangu 2015 0.29* 0.12
成都2016 Chengdu 2016 0.42** 0.56** 0.15
甘谷2016 Gangu 2016 0.56** 0.47** 0.27* 0.56**

Fig. 1

Frequency distributions for stripe rust MDS in Mingxian169/Holdfast RIL population a: Zhongliang 2015; b: Chengdu 2015; c: Gangu 2015; d: Chengdu 2016; e: Gangu 2016; f: mean MDS across five environments."

Table 2

ANOVA of MDS for stripe rust in Mingxian 169/ Holdfast RIL population"

变异来源
Source of variation
自由度
df
均方
MS
F
F-value
重复Replicate 2 7670 28.4**
环境 Environment (E) 4 46189 170.9**
基因型 Genotype (G) 287 1558 5.8**
基因型×环境 G×E 1148 459 1.7**
误差 Error 1435 270

Fig. 2

Distributions of polymorphic SNPs in Mingxian 169/ Holdfast RIL population"

Fig. 3

LOD contours of QTL on 5AL and 7AL chromosomes for adult-plant resistance to stripe rust in Mingxian 169/Holdfast RIL population"

Fig.4

Allelic effects of Qyr.gaas-5AL andQyr.gaas-7AL for stripe rust resistance in Mingxian 169/Holdfast RIL population *Significant at P<0.05."

Supplementary Table 1

Number of favorable alleles and MDS for the RILs from Mingxian 169/Holdfast population"

株系
Line
QYr.gaas-5AL
QYr.gaas-5AL
QYr.gaas-7AL
QYr.gaas-7AL
优异等位基因数目
No. of favorable alleles
最大严重度
MDS
HXF5-1 + + 2 39
HXF5-2 + - 1 63
HXF5-3 + + 2 40
HXF5-4 - + 1 82
HXF5-5 - H 0 46.5
HXF5-6 + H 1 54.5
HXF5-8 + H 1 42.5
HXF5-10 + - 1 46
HXF5-12 - - 0 32.5
HXF5-13 - - 0 75
HXF5-15 - - 0 71.5
HXF5-17 H + 1 47.5
HXF5-18 H + 1 50.5
HXF5-20 + H 1 37
HXF5-21 + + 2 63
HXF5-22 + - 1 42
HXF5-23 + + 2 62
HXF5-24 + H 1 49.5
HXF5-25 - - 0 61
HXF5-26 - - 0 63
HXF5-27 - H 0 65.5
HXF5-29 - + 1 55
HXF5-30 + + 2 73.5
HXF5-32 - - 0 69
HXF5-34 - - 0 62
HXF5-36 + - 1 60
HXF5-38 + - 1 46.5
HXF5-39 - H 0 73
HXF5-40 + - 1 66.5
HXF5-41 - H 0 54
HXF5-43 + H 1 61
HXF5-44 + - 1 51
HXF5-45 + - 1 59
HXF5-46 - + 1 51
HXF5-47 - + 1 57
HXF5-48 - + 1 56.5
HXF5-49 + + 2 47.5
HXF5-50 - + 1 70
HXF5-52 - H 0 69
HXF5-53 H + 1 35.5
HXF5-54 - - 0 38
HXF5-57 - H 0 52.5
HXF5-58 - + 1 34.4
HXF5-60 - - 0 67.5
HXF5-62 + - 1 68
HXF5-63 - - 0 75.5
HXF5-64 + - 1 59.5
HXF5-65 - - 0 76.5
HXF5-67 + - 1 67.5
HXF5-68 + - 1 58
HXF5-69 - - 0 72.5
HXF5-71 - + 1 67.5
HXF5-73 - H 0 66.5
HXF5-74 - H 0 59
HXF5-76 - - 0 63.5
HXF5-77 + - 1 63
HXF5-78 + H 1 64.5
HXF5-79 H - 0 79.5
HXF5-81 + - 1 64
HXF5-82 + + 2 35
HXF5-83 H - 0 72
HXF5-84 + - 1 56.5
HXF5-85 + H 1 63.5
HXF5-86 + - 1 55
HXF5-87 - + 1 65.5
HXF5-88 - + 1 87.5
HXF5-89 + + 2 56.5
HXF5-90 + + 2 49
HXF5-94 + - 1 37
HXF5-98 - + 1 63
HXF5-99 - - 0 62
HXF5-100 H - 0 63.5
HXF5-101 - + 1 77
HXF5-102 - H 0 66
HXF5-103 - H 0 58
HXF5-104 - + 1 59.5
HXF5-106 + + 2 60.5
HXF5-107 - - 0 72.5
HXF5-108 + H 1 71
HXF5-109 + + 2 53.5
HXF5-110 + + 2 75
HXF5-111 + + 2 54
HXF5-114 - + 1 87
HXF5-115 - + 1 77
HXF5-119 + - 1 34.5
HXF5-120 - + 1 55
HXF5-121 - H 0 55
HXF5-124 + + 2 56.5
HXF5-125 H H 0 48.5
HXF5-126 + + 2 56.5
HXF5-127 + + 2 47
HXF5-128 + - 1 60.5
HXF5-130 - - 0 65
HXF5-131 - - 0 75
HXF5-132 + + 2 65
HXF5-135 - - 0 77
HXF5-136 - - 0 72
HXF5-138 - - 0 48
HXF5-141 - + 1 69
HXF5-142 + + 2 58
HXF5-143 - - 0 53
HXF5-144 + - 1 46
HXF5-145 - - 0 70.5
HXF5-147 - + 1 65
HXF5-150 H - 0 48
HXF5-151 + - 1 54.5
HXF5-152 - + 1 62.5
HXF5-153 + - 1 69
HXF5-156 + + 2 61.5
HXF5-157 - - 0 52.3
HXF5-158 - + 1 78.5
HXF5-159 - - 0 61
HXF5-160 - - 0 82
HXF5-161 - + 1 73.5
HXF5-162 - + 1 65.5
HXF5-163 H - 0 50.5
HXF5-164 H - 0 64
HXF5-165 - - 0 69
HXF5-166 + - 1 54
HXF5-167 - + 1 60.5
HXF5-168 + + 2 51.7
HXF5-171 - - 0 70.5
HXF5-173 - - 0 72.5
HXF5-174 - - 0 69.5
HXF5-175 + - 1 58.5
HXF5-176 - + 1 70
HXF5-177 - - 0 72
HXF5-178 + - 1 80
HXF5-179 + + 2 48.5
HXF5-180 H + 1 75.5
HXF5-181 + - 1 56.5
HXF5-182 - - 0 41.5
HXF5-183 + + 2 46
HXF5-184 + - 1 57
HXF5-185 + + 2 61.5
HXF5-186 - + 1 70.5
HXF5-187 + + 2 59
HXF5-189 - - 0 69
HXF5-191 + - 1 57
HXF5-192 + + 2 36.5
HXF5-193 - - 0 52.5
HXF5-194 + + 2 75.5
HXF5-195 - + 1 59
HXF5-196 + - 1 47.5
HXF5-200 - - 0 66.5
HXF5-201 + - 1 33
HXF5-201 + + 2 31
HXF5-202 - - 0 64
HXF5-204 + - 1 53
HXF5-208 + - 1 72
HXF5-210 - - 0 70.5
HXF5-211 + - 1 70
HXF5-212 + - 1 88.5
HXF5-212 - - 0 88.5
HXF5-212 - + 1 88.5
HXF5-213 - - 0 79
HXF5-214 + + 2 81
HXF5-216 - - 0 78.5
HXF5-218 - - 0 132
HXF5-220 H + 1 54.5
HXF5-221 + - 1 59
HXF5-222 - - 0 69.5
HXF5-223 - - 0 78.5
HXF5-224 + + 2 45
HXF5-227 H - 0 68
HXF5-228 - - 0 66
HXF5-229 - + 1 43
HXF5-230 + - 1 54
HXF5-231 + - 1 29.6
HXF5-232 H + 1 73
HXF5-234 - - 0 63
HXF5-235 + + 2 51
HXF5-236 - - 0 65
HXF5-238 + + 2 50
HXF5-239 - - 0 54
HXF5-240 + + 2 57
HXF5-241 - - 0 65
HXF5-242 + - 1 56
HXF5-243 - - 0 77
HXF5-244 - - 0 79
HXF5-245 + - 1 76.5
HXF5-246 + - 1 62.5
HXF5-247 - + 1 55
HXF5-248 - - 0 69.5
HXF5-249 + + 2 57
HXF5-250 - - 0 60.5
HXF5-251 + + 2 43.5
HXF5-252 + - 1 44
HXF5-253 + + 2 66
HXF5-254 - - 0 68.5
HXF5-255 - - 0 68
HXF5-256 - - 0 64
HXF5-257 + + 2 61
HXF5-258 H - 0 63
HXF5-260 - - 0 52.5
HXF5-261 - - 0 72.5
HXF5-262 - - 0 70.5
HXF5-263 - + 1 63.5
HXF5-264 + + 2 55
HXF5-267 - + 1 63.5
HXF5-268 - - 0 83.5
HXF5-271 - - 0 55
HXF5-273 + + 2 49.5
HXF5-274 + + 2 42.5
HXF5-275 - + 1 66
HXF5-276 + + 2 62
HXF5-277 + - 1 65
HXF5-278 + - 1 64
HXF5-279 - - 0 63
HXF5-283 - + 1 79
HXF5-284 - - 0 71
HXF5-285 H - 0 78
HXF5-286 + + 2 50
HXF5-287 - - 0 59.5
HXF5-288 + + 2 66
HXF5-289 - - 0 71.5
HXF5-290 + - 1 55.5
HXF5-291 + - 1 49.5
HXF5-292 + - 1 80.5
HXF5-293 - + 1 66.5
HXF5-294 + - 1 69
HXF5-295 + - 1 68.5
HXF5-296 + - 1 69.5
HXF5-297 - - 0 80.5
HXF5-299 - - 0 73
HXF5-301 - - 0 60.5
HXF5-302 - - 0 53.5
HXF5-303 H - 0 70.5
HXF5-304 + + 2 57
HXF5-305 - - 0 52.5
HXF5-306 + - 1 60
HXF5-307 + - 1 72
HXF5-308 - + 1 63.5
HXF5-309 - - 0 59.5
HXF5-310 + - 1 59.5
HXF5-312 - + 1 59
HXF5-313 - - 0 68
HXF5-315 - - 0 35
HXF5-316 + - 1 64
HXF5-317 - - 0 71
HXF5-319 + + 2 44.5
HXF5-320 - + 1 62
HXF5-321 - - 0 80.5
HXF5-322 - - 0 88
HXF5-323 - + 1 49
HXF5-324 + + 2 58
HXF5-325 - + 1 82.5
HXF5-326 - - 0 66
HXF5-327 - - 0 67
HXF5-328 - + 1 75
HXF5-329 - - 0 66.5
HXF5-330 + - 1 66.5
HXF5-331 + - 1 68
HXF5-332 - - 0 66.5
HXF5-333 - - 0 67.5
HXF5-334 - - 0 77.5
HXF5-335 - + 1 84.5
HXF5-336 + - 1 62.5
HXF5-337 - - 0 57.5
HXF5-338 + - 1 54.5
HXF5-340 + - 1 66.5
HXF5-341 - - 0 63
HXF5-342 - - 0 66.5
HXF5-343 - - 0 56
HXF5-344 - - 0 54.5
HXF5-346 + - 1 74.5
HXF5-347 + - 1 62.5
HXF5-349 - - 0 80.5
HXF5-350 + - 1 68.5
HXF5-351 - - 0 53.5
HXF5-352 - + 1 59.5
HXF5-353 - - 0 56.5
HXF5-354 + - 1 47
HXF5-355 - - 0 67.5
HXF5-356 - - 0 57.5
HXF5-357 + - 1 52
HXF5-358 - + 1 38.5
HXF5-359 - - 0 56
HXF5-361 + + 2 69
HXF5-362 + - 1 66
HXF5-363 + - 1 64
HXF5-364 + + 2 55
HXF5-365 - - 0 61
HXF5-366 - - 0 73.5
HXF5-367 - - 0 74.5
HXF5-370 + + 2 45
HXF5-371 + - 1 78.5
HXF5-886 + - 1 69

Supplementary Fig. 1

MDS for stripe rust evaluated in Mingxian169/Holdfast RIL population"

Supplementary Fig. 2

Genotyping of KASP markers for Ax-109948955 (5A) (a) and Ax-11036106 9 (7A) (b) Red dot indicates lines with the same genotype as the susceptible parent Mingxian169, whereas blue ones show lines with the same genotype as the resistant parent Holdfast, black ones are water control and green ones indicate the heterozygous genotype."

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