Validation of gene based marker-QTL association for grain dimension traits in rice
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ORIGINAL ARTICLE
Validation of gene based marker-QTL association for grain dimension traits in rice Deepti Anand & Mamta Baunthiyal & Ashutosh Singh & S. Gopala Krishnan & N. K. Singh & K. V. Prabhu & A. K. Singh
Received: 19 July 2012 / Accepted: 8 November 2012 # Society for Plant Biochemistry and Biotechnology 2012
Abstract Validation of marker-QTL association for genes grain size 3 (GS3), grain weight 2 (GW2), seed width 5 (qSW5) and a QTL qgrl7.1 for grain length was undertaken in a set of 242 diverse rice germplasm. Further, the study was extended to an F2 mapping population derived from cross of Sonasal, a short grain aromatic rice landrace with Pusa Basmati 1121, a variety with extra long slender grains. Seven gene specific markers, namely, SF28, SR17, RGS1and RGS2 based on GS3, W004 for GW2, MS40671 for qSW5 and RM505 for qgrl7.1, were used for validation. Single marker analysis revealed significant association of these markers to grain size and shape. The marker SF28 explained highest phenotypic variance (37 %) while the marker W004 explained lowest variance (2.6 %) for grain length in the germplasm set at the significance level P3.3 mm (Shomura et al. 2008). The model for japonica rice domestication proposed by them suggested that the qSW5 gene propagated to upland areas of China and Japan, is absent in wild species O. rufipogon and indica rices. Also, deletion in the gene identified through comparative sequencing clearly associated the increase in grain width due to Nipponbare allele (japonica). In our study, the marker MS40671 based on qSW5 grouped the rice germplasm into two allelic groups of 320 bp and 300 bp
Table 4 Per cent phenotypic variance (R2) explained by different markers linked to grain dimension traits in germplasm and F2 population Markers
Grain Dimension traits RRL
RRB
RRL/B
MRL
MRB
MRL/B
CKL
ER
GP
F2
GP
F2
GP
F2
GP
F2
GP
F2
GP
F2
GP
F2
GP
F2
SF28 SR17 RGS1 RGS2 W004 MS40671
37.0 7.9 12.0 6.3 NS 6.3
16.0 NS
10.0 NS 6.0 5.4 NS NS
3.0 NS
32 4.2 14.0 8.6 NS 7.5
14.0 NS
7.0 4 13 13.8 NS 2.6
32.5 NS
6.0 NS 4 2.5 NS 2.6
4.5 NS
33.0 NS 14 12.9 NS 5.1
28.0 NS
32 4.2 8 8.6 NS 6.3
25.0 2.7
12 NS NS NS NS NS
NS 3.7
RM505
17
4.51
NS
NS
12.4
NS
8.1
5.4
NS
NS
8.7
8.8
12.6
3.5
NS
NS
RRL Rough rice length; RRB Rough rice breadth; RRL/B Rough rice length breadth ratio; MRL Milled rice length; MRB Milled rice breadth; MRL/B Milled rice length breadth ratio; CKL Cooked kernel length; ER Elongation ratio; GP Germplasm; F2: F2 population derived from Sonasal/Pusa Basmati 1121; NS Not significant
J. Plant Biochem. Biotechnol.
but its contribution to the phenotypic variance for grain width was very low indicating that qSW5 locus was not widely distributed in the germplasm studied. The marker RM505 flanking the QTL qgrl7.1 classified the rice germplasm into two allelic groups comprising of 220 bp and 180 bp fragment size and explained 12.4 % and 12.6 % phenotypic variance for grain L/B ratio and cooked kernel length, respectively. Recently, this
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