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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (10): 2633-2642.doi: 10.3724/SP.J.1006.2023.32007

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

QTL identification and favorable allele mining of cold tolerance at seedling stage by reciprocal introgression and recombinant inbred line populations in rice

CAO Hui-Min1,2(), YANG Xian-Li3(), WANG Li-Zhi3, LI Ping-Ping1, ZHAI Lai-Yuan2, JIANG Shu-Kun3, ZHENG Tian-Qing2, QIU Xian-Jin1(), XU Jian-Long2,4,5()   

  1. 1Key Laboratory of Sustainable Crop Production in the Middle Researches of the Yangtze River, Ministry of Agriculture and Rural Affairs (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China
    4Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong, China
    5Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China
  • Received:2023-02-16 Accepted:2023-04-17 Online:2023-10-12 Published:2023-04-24
  • Contact: E-mail: xjqiu216@yangtzeu.edu.cn; E-mail: xujianlong@caas.cn
  • About author:**Contributed equally to this work
  • Supported by:
    Shenzhen Basic Research Special Project(JCYJ20200109150713553);Hainan Yazhou Bay Seed Lab Project(B21HJ0216)

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Abstract:

Cold damage often hinders rice growth, affects its morphogenesis and leads finally to serious yield loss. Identifying favorable genes tolerant to cold, and breeding elite rice varieties with cold tolerance is an effective way to solve this problem. In this study, two sets of reciprocal introgression lines and a set of recombinant inbred line derived from xian variety Minghui 63 and geng variety 02428 were evaluated for cold tolerance in climate chamber using cold tolerance-related traits such as wilting degree and survival rate after recovered growth. Combined with the available Bin genotype data generated by previous re-sequencing, 13 QTLs for cold tolerance at seedling stage were identified on chromosomes 1, 4, 5, 7, and 12, which explained 0.36% to 13.63% of phenotypic variation. No QTL was stably detected in different genetic backgrounds, whereas five QTLs were simultaneously detected for both wilting degree and survival rate on chromosomes 1, 5, 7, and 12. Among them, QTLs in the regions of 12,732,139-13,202,097 bp and 14,445,778-14,585,009 bp on chromosome 1, and 14,658,891-15,684,510 bp on chromosome 5 had high LOD values above 25 and were considered as reliable main-effect QTLs. Combined with gene annotation, gene expression profile and phenotyping data of cold tolerance of 3K germplasms, the previously cloned gene OsWKRY45 for cold tolerance was regarded as the responsible gene for the QTL in the region of 14,658,891-15,684,510 bp on chromosome 5, while the two candidate genes, LOC_Os01g25540 and LOC_Os01g25560 in the two regions on chromosome 1, were the new candidate genes for both wilting degree and survival rate. Haplotype analysis indicated that Hap2, Hap4, and Hap9 of LOC_Os01g25540 and Hap1, Hap8, and Hap10 of LOC_Os01g25560 were favorable haplotypes for cold tolerance. The results provide the novel germplasms and favorable genes for molecular improvement of cold tolerance in rice.

Key words: rice, cold tolerance at seedling stage, wilting degree, QTL mapping, haplotype

Fig. 1

Frequency distribution of MH63 genome in the reciprocal introgression line and recombinant inbred line populations"

Table 1

Performance of cold tolerance at seedling stage of the parents, reciprocal introgression lines and recombinant inbred lines"

性状
Trait		 明恢63
MH63		 02428 明恢63背景导入系 MH63-ILs 02428背景导入系 02428-ILs 重组自交系 RIL
平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range		 平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range		 平均值±标准差
Mean ± SD		 峰度
Kurtosis		 偏度
Skewness		 变幅
Range
枯萎度
Wilting degree		 8.00 1.00** 8.40±
1.60		 10.07 -3.17 1.00-
9.00		 6.15±
2.91		 -1.30 -0.48 1.00-
9.00		 8.20±
1.80		 6.78 -2.65 1.00-
9.00
存活率
Survival rate (%)		 15.69 81.90** 6.00±
17.00		 12.63 3.53 0-
100.00		 35.00±
36.00		 -1.19 0.58 0-
100.00		 8.00±
20.00		 7.91 2.87 0-
100.00

Fig. 2

Frequency distribution of cold tolerance at seedling stage in the three populations derived from MH63 and 02428"

Table 2

QTLs for cold tolerance at seedling stage in the three populations derived from MH63 and 02428"

群体
Population		 性状
Trait		 染色体
Chr.		 QTL 区间
Interval (bp)		 LOD 加性效应
A		 贡献率
PVE (%)
明恢63背景导入系
MH63-ILs		 枯萎度WD 5 qWD5 14,658,891-15,684,510 28.72 -1.65 8.17
存活率SR 5 qSR5 14,658,891-15,684,510 29.43 0.18 5.86
12 qSR12.1 24,001,167-24,472,105 3.95 0.20 3.28
02428背景导入系
02428-ILs		 枯萎度WD 4 qWD4 1,048,077-1,157,529 7.20 1.15 12.92
12 qWD12 26,529,940-26,660,385 3.03 -0.67 5.20
存活率SR 4 qSR4 764,097-963,403 7.42 −0.15 13.63
12 qSR12.2 26,529,940-26,660,385 2.73 0.08 4.75
重组自交系
RIL		 枯萎度WD 1 qWD1.1 12,732,139-13,202,097 44.95 1.57 9.58
1 qWD1.2 14,445,778-14,585,009 31.63 -1.25 5.91
7 qWD7 16,793,414-17,068,785 2.64 -0.28 0.36
存活率SR 1 qSR1.1 12,732,139-13,202,097 49.88 -0.19 10.67
1 qSR1.2 14,445,778-14,585,009 36.09 0.15 6.71
7 qSR7 16,793,414-17,068,785 3.08 0.03 0.40

Fig. 3

Distribution of QTLs detected for cold tolerance at seedling stage in the three populations derived from MH63 and 02428 WD: wilting degree; SR: survival rate."

Fig. 4

Haplotype analysis of two candidate genes A, D: phenotypic difference between different haplotypes of the two cold tolerance traits, the different lowercase letters indicate significant differences among different haplotypes at the 0.01 probability level; B, E: frequency distribution of five subpopulations in the different haplotypes; C: the relative expression level of LOC_os01g22540 of leaf of Kongyu 131 at seedling stage under cold and normal conditions (data reported by Yu et al. [18]); F: the relative expression level of LOC_os01g22560 of root of Nipponbare at seedling stage under cold and normal conditions (data reported by Yu et al. [18]); ** and *** represent significant difference at the 0.01 and 0.001 probability levels, respectively."

Table S1

Haplotype information of the two candidate genes"

候选基因
Candidate gene		 单倍型编号
Hap ID		 单倍型
Haplotype (5′-3′)		 种质资源数目 No. of accessions
籼稻
xian		 粳稻
geng		 Aus Bas 中间型
Admix
LOC_Os01g25540 Hap1 GCTATTGGACCAGAACCCGTAGGAGGCCACCTGCAGCCACTGCAGCGAAGCGAG 110 4 37 9 4
Hap2 GAGACTGGATCGGATCCCGTGGGGGGCTGCCTATAGCCACTGTGGCAAAGCGGA 1 138 0 1 3
Hap3 TCGATTAGACCAGAACTAGTAGGAGGCCACCTGCAGCCACTGTGGCGAAGCGGA 123 0 0 0 2
Hap4 TCGATTAGGCCAGAACCAGTAGGAGGTCACCTGCAGCCACTGTGGAGAAGCGGA 96 0 0 0 1
Hap5 GAGGCCGGATTAAACCCCGTGGAGGGCCACCTATAGCCACTGTGTAGAAGCGGG 37 0 40 1 4
Hap6 TCGATTGAACCAGAACCCGTAGGGGGCCACTTGCAGCCACAGTGGAGAAACGGA 57 0 0 0 1
Hap7 GAGGCTGGATTAGACCCCATGGGGGGTCATCTATGGCTACTGTAGCGAAGCGGG 49 0 0 0 2
Hap8 GCTATTGGACCAGAACCCGTAGGAGGCCACCTGCAGCCACTGTAGCGAAGCGAG 42 0 0 0 0
Hap9 GAGACTGGATCGGATCCCGTGGGGGACTGCCTATAGCCACTGTGGCAAAGCGGA 0 28 0 0 2
LOC_Os01g25560 Hap1 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCCAAG 5 344 0 8 14
Hap2 TCCGGTGCAGAGCTGGGAGCGTTAGCGTTCCTATCAGG 155 0 0 0 3
Hap3 TTCGGCGCAGAGCTGGGGGCGCTGGCGGCCCTATCAGG 136 3 12 0 3
Hap4 TCAGGCGCAGAGCTGGGAGCGTTAGCGGCCCTATCAGG 109 0 0 0 0
Hap5 TCCGGCGCAGAGCTGGAAGCGTTAGCGGCCCTATCAGG 89 0 0 0 0
Hap6 TCCGGCGCAGAGCTAAGAGCGTTAACGGCCCGATCAGA 29 0 52 0 5
Hap7 TCCGACGCAGAGCTGGGAGCGTTAGCCGCCCTATCAGG 41 0 33 7 2
Hap8 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCCMAG 1 76 0 0 2
Hap9 TCCGGCGCAGAGCTGAGATCGTTAGCGGCTCTATTAGG 60 0 1 0 1
Hap10 ACCAGCGCGCGATCGGGAGCTTCAGTGGCCCTTCC-AG 1 37 0 3 6
Hap11 TTCGGCGCAGAGCTGGGGGCGCTGGCGGCCCTATC-GG 31 0 3 0 0
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