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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (8): 1174-1184.doi: 10.3724/SP.J.1006.2020.92066

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

Detection of QTLs controlling cold tolerance at bud bursting stage by using a high-density SNP linkage map in japonica rice

JIANG Shu-Kun1,*(),WANG Li-Zhi1,YANG Xian-Li1,LI Bo2,MU Wei-Jie3,DONG Shi-Chen3,CHE Wei-Cai3,LI Zhong-Jie1,CHI Li-Yong1,LI Ming-Xian1,ZHANG Xi-Juan1,JIANG Hui2,LI Rui1,ZHAO Qian1,LI Wen-Hua2,*()   

  1. 1Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences/Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region/Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, Heilongjiang, China
    2Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China
    3Life Science and Technology College, Harbin Normal University, Harbin 150025, Heilongjiang, China
  • Received:2019-12-08 Accepted:2020-03-24 Online:2020-08-12 Published:2020-04-10
  • Contact: Shu-Kun JIANG,Wen-Hua LI E-mail:sk_jiang@126.com;nkylwh@163.com
  • Supported by:
    National Key Research and Development Program of China(2018YFD0300105-5-2);National Natural Science Foundation of China(31661143012);Provincial Funding for the National Key Research and Development Program in Heilong jiang Province(768001);Natural Science Foundation of Heilongjiang Province of China(YQ2019C020);Heilongjiang Province Agricultural Science and Technology Innovation Project(2018CQJC002);Heilongjiang Province Agricultural Science and Technology Innovation Project(2019CQJC002)

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Abstract:

Direct seeded rice (DSR) has received much attention because of its time- and labour-saving and low-input demand. However, the long-term cultivation method of seedling-transplantation has led to loss of some low-temperature-tolerant genes expressed at the bud stage. It has made many currently popular rice varieties unsuitable for direct seeding production. Therefore, it is important to identify cold-tolerance genes at the bud stage and to provide genes for subsequent molecular marker assistant breeding. In this study, we used a recombinant inbred line population constructed by cross of Lijiangxintuanheigu (LTH) and Shennong 265 (SN265) and its linkage map containing 2818 markers to detect cold tolerance QTLs at the bud stage. A total of five QTLs were detected on rice chromosomes 1, 3, 9, and 11. All the cold tolerance alleles were from the cold-tolerant parent LTH. The LOD values of these QTLs ranged from 3.05 to 24.01, and the phenotypic variations ranged from 8.0% to 53.5%. Among them, the major QTL qCTB11b was located in a 790 kb interval of 21.24 Mb to 22.03 Mb on the long arm of chromosome 11. Subsequently, the “selective mapping” strategy was used for QTL verification and pyramiding effect analysis. Genetic improvement of cold tolerance at the bud stage would be achieved through pyramiding more QTLs. These results not only promote people’s understanding of the genetic basis for cold tolerance at the bud stage in rice but also provide theoretical basis and technical guidance for genetic improvement of DSR varieties.

Key words: japonica rice, cold tolerance at bud bursting stage, re-sequencing, genetic map, QTLs

Fig. 1

Physical map (A) and genotype (B) of Lijiangxintuanheigu-shennong 265 (LTH-SN265) RIL population Physical position is based on MSU Rice Genome Annotation Project Release 7 sequence. Yellow: SN265 genotype; Blue: LTH genotype."

Fig. 2

Evaluation criteria for chilling injury at rice bud stage SN265: Shennong 265; LTH: Lijiangxintuanheigu."

Fig. 3

Comparison of no cold treatment (A) and cold treatment (B) at bud bursting stage between LTH and SN265"

Fig. 4

Distribution of cold tolerance at bud bursting stage in LTH-SN265 RILs"

Table 1

QTLs controlling cold tolerance at bud bursting stage identified in LTH-SN265 RILs"

数量性状
基因座
QTL		 染色体
Chr.		 峰值位置a
Peak pos.a		 峰值标记
Peak marker		 QTL区间QTL interval LOD值
LOD value		 表型贡献率
Var. (%)		 加性
效应
Add.		 增效等位
基因来源
Positive
allele
物理图谱
Physical (Mb)		 定位区间
Location
interval (Mb)
qCTB1 1 0.73 Bin01-002 0.43-0.93 0.50 3.26 8.20 0.22 LTH
qCTB3 3 29.40 Bin03-281 29.40-32.87 3.47 3.05 8.00 0.21 LTH
qCTB9 9 21.45 Bin09-185 19.90-22.30 2.40 5.36 16.60 0.34 LTH
qCTB11a 11 9.71 Bin11-087 8.53-9.93 1.40 8.58 24.10 0.39 LTH
qCTB11b 11 21.80 Bin11-141 21.24-22.03 0.79 24.01 53.50 0.64 LTH

Fig. 5

Chromosome location of putative QTL for cold tolerance at bud bursting stage in LTH-SN265 RILs OsCOIN: cold inducible zinc finger protein[46]; OsHOS1: a rice E3-Ubiquitin Ligase in the modulation of cold stress response[47]; OsDREB1A, OsDREB1B: cold inducible AP2/EREBP transcription factor gene[48]; qCTP11: a QTL for cold tolerance at bud stage[27]."

Fig. 6

Genotype of recombinant plant for validating cold tolerance QTL and analyzing pyramiding effect at bud busting stage “-”: missing."

Fig. 7

Effect of cold tolerance QTL and pyramiding effect at bud stage in LTH-SN265 RILs A: Shennong 265 (SN265); B: Lijiangxintuanheigu (LTH); C-G: Cold tolerance effect of qCTB1, qCTB3, qCTB9, qCTB11a, and qCTB11b at bud stage; H: Cold tolerance cluster effect of qCTB1 and qCTB3 at bud stage; I: Cold tolerance cluster effect of qCTB3 and qCTB9 at bud stage; J: Cold tolerance cluster effect of qCTB9 and qCTB11a at bud stage; K: Cold tolerance cluster effect of qCTB11a and qCTB11b at bud stage; L: Cold tolerance cluster effect of qCTB11a and qCTB11b at bud stage; M: Cold tolerance cluster effect of qCTB9 and qCTB11b at bud stage; N: Cold tolerance cluster effect of qCTB1, qCTB3, and qCTB9 at bud stage; O: Cold tolerance cluster effect of qCTB3, qCTB9, and qCTB11a at bud stage; P: Cold tolerance cluster effect of qCTB1, qCTB3, and qCTB11a at bud stage; Q: Cold tolerance cluster effect of qCTB1, qCTB11a, and qCTB11b at bud stage; R: Cold tolerance cluster effect of qCTB3, qCTB11a, and qCTB11b at bud stage; S: Cold tolerance cluster effect of qCTB9, qCTB11a, and qCTB11b at bud stage; T: Cold tolerance cluster effect of qCTB1, qCTB3, qCTB11a, and qCTB11b at bud stage; U: Cold tolerance cluster effect of qCTB1, qCTB9, qCTB11a and qCTB11b at bud stage; V: Cold tolerance cluster effect of qCTB3, qCTB9, qCTB11a, and qCTB11b at bud stage; W: Cold tolerance cluster effect of qCTB1, qCTB3, qCTB9, qCTB11a, and qCTB11b at bud stage; X: none QTL line."

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