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Identification of candidate genes for grain number in rice (Oryza sativa L.)

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Abstract

Large number of well-filled grains per panicle is an important yield component trait in rice. A combination of QTL mapping and transcriptome profiling was used to identify candidate genes for grain number. A framework linkage map was constructed using 166 SSR markers evenly distributed over the 12 rice chromosomes. QTL mapping using 3 years phenotyping data on a set of recombinant inbred lines derived from a cross between Pusa 1266 (high grain number) and Pusa Basmati 1 (low grain number) identified one consistent QTL qGN4-1 on the long arm of chromosome 4 with major effect on grain number. This QTL was co-localized with major QTLs for primary and secondary branches per panicle, and number of panicles per plant. The QTL interval was narrowed down to 11.1 cM (0.78 Mbp) by targeted enrichment of the region with six additional markers. Microarray transcriptome profiling revealed eight genes in the qGN4-1 region differentially expressed between the two parents during early panicle development. Synteny of this QTL and potential candidates was examined in wheat, barley, maize, sorghum, and Brachypodium to further validate the association.

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Acknowledgements

We are thankful to the Department of Biotechnology, Government of India for financial support of the grant BT/AB/03/FG-2/2003.

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Authors and Affiliations

  1. Rice Genome Laboratory, National Research Centre on Plant Biotechnology, New Delhi, 110012, India

    Rupesh Deshmukh, Abhinay Singh, Neha Jain, Shweta Anand, Kishor Gaikwad, Tilak Sharma, Trilochan Mohapatra & Nagendra Singh

  2. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India

    Ashok Singh

  3. Swami Ramanand Teerth Marathwada University, Nanded, 431606, India

    Rupesh Deshmukh & Raju Gacche

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  1. Rupesh Deshmukh
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  2. Abhinay Singh
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  3. Neha Jain
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  4. Shweta Anand
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  5. Raju Gacche
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  6. Ashok Singh
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  7. Kishor Gaikwad
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  9. Trilochan Mohapatra
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  10. Nagendra Singh
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Correspondence to Nagendra Singh.

Electronic supplementary material

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Table S1

Details of primers used for qRT-PCR analysis of eight candidate genes using RNA samples isolated from early stage primordia from Pusa 1266 and Pusa Basmati1 (DOC 69 kb)

Table S2

Correlation coefficients of grain number (GN) and associated traits (PB = Primary branches, SB = Secondary branches, PL = Panicle length, and NP = Number of panicles), in 161 RILs from Pusa 1266/Pusa Basmati 1 cross in 3 years (DOC 70 kb)

Table S3

Details of primers used to narrow down the grain number QTL qGN4-1 in the marker interval RM2441-HvSSR04-49 on rice chromosome 4 (DOC 68 kb)

Table S4

Functional annotation of eight differentially expressed candidate genes in QTL region qGN4-1 (DOC 538 kb)

Table S5

Details of single nucleotide polymorphismSNP and insertion/deletionInDel observed in Pusa 1266/Pusa Basmati 1 by pairwise DNA sequence alignment of the promoter regions of eight differentially expressed genes in the qGN4-1 region after resequencing (DOC 529 kb)

Fig. S1

Frequency distribution of primary branches per panicle in RIL population derived from cross between Pusa 1266 (P1) and Pusa Basmati 1 (P2) in three different years (DOC 113 kb)

Fig. S2

Frequency distribution of secondary branches per panicle in RIL population derived from cross between Pusa 1266 (P1) and Pusa Basmati 1 (P2) in three different years (DOC 125 kb)

Fig. S3

Frequency distribution of panicle length in RIL population derived from cross between Pusa 1266 (P1) and Pusa Basmati 1 (P2) in three different years (DOC 130 kb)

Fig. S4

Frequency distribution of panicle number in RIL population derived from cross between Pusa 1266 (P1) and Pusa Basmati 1 (P2) in three different years (DOC 124 kb)

Fig. S5

Molecular genetic linkage map of 172 markers (166 from initial mapping and 6 addition markers in the qGN4-1 region) developed using 161 RILs derived from the cross between Pusa 1266 and Pusa Basmati 1. Distance between markers were based on Kosambi function and calculated using MultiPoint 1.2 software (DOC 87 kb)

Fig. S6

Chromatogram of QTLs detected for the grain number and associated traits across 3 years in RIL population derived from the cross between Pusa 1266 and Pusa Basmati 1 by using QTL cartographer 2 showing LOD score and additive effect of loci (DOC 96 kb)

Fig. S7

Chromatogram of QTLs detected for the grain number per panicle across 3 years in RIL population derived from the cross between Pusa 1266 and Pusa Basmati 1 A QTL interval detected at first step of mapping using linkage map of 166 molecular markers, B which further narrowed down by using six newly designed markers (DOC 104 kb)

Fig. S8

Frequency distribution of grain number in 537 F2 progenies derived from Pusa 1266/Pusa Basmati 1 cross, screened for HvSSR04-40 and HvSSR04-46 markers flanking the grain number QTL qGN4-1 (DOC 98 kb)

Fig. S9

Gene colinearity between qGN4-1 region of rice chromosome 4 and other cereals. Dotted lines indicate the position of orthologous genes in maize, sorghum, and brachypodium and mapped ESTs in barley and wheat. Gene ID corresponds to the last digits of the TIGR rice (prefix LOC_Os04g, www.rice.plantbiology.msu.edu), Maize sequence (prefix GRMZM2G, www.maizesequence.org), Phytozome sorghum (prefix Sb01g, www.phytozome.net), and Brachypodium (prefix Bradi4g, www.brachybase.org) (DOC 81 kb)

Fig. S10

Pairwise DNA sequence alignment of Pusa 1266 and Pusa Basmati 1 at promoter regions of eight differentially expressed genes in the qGN4-1 region of rice (DOC 84 kb)

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Deshmukh, R., Singh, A., Jain, N. et al. Identification of candidate genes for grain number in rice (Oryza sativa L.). Funct Integr Genomics 10, 339–347 (2010). https://doi.org/10.1007/s10142-010-0167-2

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