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. 2017 Dec;10(1):28.
doi: 10.1186/s12284-017-0167-0. Epub 2017 Jun 5.

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array

Shanmugavadivel Ps  1   2 , Amitha Mithra Sv  1 , Chandra Prakash  1 , Ramkumar Mk  1 , Ratan Tiwari  3 , Trilochan Mohapatra  4 , Nagendra Kumar Singh  5
Affiliations

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array

Shanmugavadivel Ps et al. Rice (N Y). 2017 Dec.

Abstract

Background: Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F8 recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance.

Results: To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively.

Conclusions: The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.

Keywords: Heat tolerance; Nagina22; QTL mapping; Rice; SNP.

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Figures

Fig. 1
Fig. 1
Phenotyping of F8 RIL mapping population under non-stress and heat stress conditions at ICAR-IIWBR. (a) At vegetative stage under non-stress condition (b). At reproductive stage under non-stress (c). At vegetative stage under non-stress condition inside controlled environment structure with roof top open (d). With reproductive stage heat stress for 10 days in controlled environment structure with roof top covered
Fig. 2
Fig. 2
Phenotype distributions and Correlation of stress indices. (a) Trait distribution and linear correlation values (b). Correlogram of stress indices
Fig. 3
Fig. 3
Chromosome-wise polymorphism survey using 5K SNP array and polymorphic SNPs in Nagina22 x IR64 mapping population
Fig.4
Fig.4
QTLs identified for heat tolerance in rice in the mapping population derived from Nagina22 and IR64
Fig. 5
Fig. 5
Epistatic interaction network between SNP marker loci. a STI for sterility (b). STI for yield (c). SSI for yield
See this image and copyright information in PMC

References

    1. Begum T, Reuter R, Schöffl F. Overexpression of AtHsfB4 induces specific effects on root development of Arabidopsis. Mech Dev. 2013;130(1):54–60. doi: 10.1016/j.mod.2012.05.008. - DOI - PubMed
    1. Broman KW, Wu H, Sen Ś, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003;19(7):889–890. doi: 10.1093/bioinformatics/btg112. - DOI - PubMed
    1. Buu BC, Ha PTT, Tam BP, Nhien TT, Hieu NV, Phuoc NT, Minh LT, Giang LH, Lang NT. Quantitative trait loci associated with heat tolerance in rice (Oryza sativa L.) Plant Breed Biotech. 2014;2:14–24. doi: 10.9787/PBB.2014.2.1.014. - DOI
    1. Cao L, Zhao J, Zhan X, Li D, He L, Cheng S. Mapping QTLs for heat tolerance and correlation between heat tolerance and photosynthetic rate in rice. Chin J Rice Sci. 2003;17:223–227.
    1. Carriger S, Vallee D. More crop per drop. Rice Today. 2007;6:10–13.

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