Assessment of the association between yield parameters and polymorphic sites of the Ghd7 locus in a core-set of rice cultivars grown in Sri Lanka

N D U S Nakandala,L T Ranaweera,S D S S Sooriyapathirana,S I Karunarathne,W W M U K Wijesundara,R W K M Senevirathna,R M S K Rathnayake,U A K S Udawela

doi:10.4038/cjs.v48i2.7616

N D U S Nakandala, L T Ranaweera + Show 6 more

Open Access

https://doi.org/10.4038/cjs.v48i2.7616

Copy DOI

Abstract

Yield improvement is a major aspect in rice breeding programs. Ghd7 is a pleiotropic gene which regulates yield, plant height, and heading date in rice. Although Ghd7 has been previously cloned and sequenced in several other rice cultivars, none of the studies have been conducted for Sri Lankan rice germplasm. Therefore, in this study, we assessed the yield performance of 12 rice cultivars, genetic polymorphism of Ghd7 locus and associations between DNA markers and yield traits. Breeder seeds of the selected cultivars were obtained from RRDI, Bathalagoda, and established under greenhouse conditions at Peradeniya, Sri Lanka in Maha and Yala seasons, 2017. The cultivars were subjected to morphometric analysis, genotyped for 12 DNA markers and sequenced at Seq7-8 locus. Morphometric data were subjected to single marker analysis using General Linear Model (GLM) in SAS 9.4. Here we reported six marker haplotypes based on the arrangement of 13 DNA maker alleles at Ghd7. Moreover, twenty-three SNP/INDEL variations at Seq7-8 locus revealed close genetic relationships between the rice cultivars Bg 90-2, Bg 352 and At 307, Bg310. Four polymorphic markers (Seq7-8, Seq1-2, RM5436 and RM5346) were significantly associated with rice yield traits so that they could be used in marker assisted selection. The SNPs/INDELs of Ghd7 were significantly associated with all the yield traits except 100 seed weight and 100 endosperm weight. Thus the present study demonstrate the possibility of employing marker assisted breeding to improve rice yield using the polymorphic genomic information at Ghd7 locus.

Highlights

Rice yield is a complex agronomic trait governed by both the genetic constitution of the plant and the environment (Yan et al, 2011)
For the rice cultivars, alleles with an average of 1.86 alleles per locus were detected for seven DNA markers
The genetic divergence among cultivars was well supported by DNA length polymorphism and SNP/INDEL polymorphisms

Summary

Introduction

Rice yield is a complex agronomic trait governed by both the genetic constitution of the plant and the environment (Yan et al, 2011). Ghd has been identified as one of such important QTLs, which plays a key role in improving the rice yield by simultaneous regulation of the plant height, grain number and the heading date (Xue et al.,2008). The two exon regions in Ghd encodes a CCT domain protein which contains 257 amino acids (Xing et al, 2014; Xue et al, 2008). This protein was identified in both indica rice varieties such as Minghui 63 and japonica rice varieties such as Nipponbare (Xue et al, 2008; Lu et al, 2012)

Objectives

Methods

Results

Conclusion