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The efficacy of modern rice varieties has been challenged by global warming because of their incapability to tolerate heat stress. Breeding for heat tolerance (HT) is therefore essential. Molecular breeding studies on HT in hybrid rice is sparse although HT quantitative trait loci (QTL) have been discovered. China is the leading country for hybrid rice production, however, introgression of HT alleles to hybrids is not practiced in breeding programmes. Therefore, the objectives of this study were to introgress HT alleles from indica donors Bg 90-2 and Mengguandamagu to SH 527, a popular parent in hybrid variety development, and to identify the associated DNA markers with HT to facilitate hybrid rice molecular breeding in China. The BC 2 F 2:4 introgression lines were produced by crossing donor and recurrent parents and their performances were evaluated at two provinces of China in 2011 and 2012 under normal and heat stress conditions. The data were subjected to ANOVA and HT was compared against the standard heat-check variety N22. Out of 600 SSR markers, 61 and 59 markers were polymorphic for the two crosses SH 527/ Bg 90-2 and SH 527/ Mengguandamagu, respectively and introgression lines were subsequently genotyped. The single-marker analysis was performed to detect marker trait associations. A total of 46 HT introgression lines were obtained with 88.3 % of homozygosity for HT alleles and seven high yielding HT lines were specifically selected for the provinces. Under heat stress, 42 significant marker trait associations were detected. Two of these were previously reported in HT QTLs implying their applicability in rice breeding programmes.

Plant patents (PPs) and Plant Breeders' Rights (PBR) are two forms of Intellectual Property Rights (IPRs) granted to improved novel crop varieties. The government of the state of authority issues PPs and PBR after confirming the uniqueness of varietal identity. The uniqueness relies on distinctiveness, uniformity, and stability of the new variety. Morphological, physiological and biochemical descriptors are less capable in varietal discrimination to obtain IPR in the presence of large number of closely related varieties as the reference collections, but advanced molecular tools such as DNA fingerprinting and sequencing have high potentials to detect the uniqueness. DNA fingerprinting and sequencing have identified varietal identities of many crops such as rice, apple, wheat, and soybean revealing the potential of the successful use of molecular descriptors in granting patents or PBR. The novelty verification is the first step in the process of allowing patents or PBRs. The patent or plant variety protection office requires an application from the breeder that includes all the details of the plant variety fulfilling all statutory requirements to grant varietal ownership via a patent certificate or a plant variety protection certificate. Currently, Sri Lanka has no developed system of IPRs to allow PBR or patents for improved crop varieties. The efforts made by breeders in developing novel varieties can be justified and appreciated by granting plant varietal ownerships. For this purpose, molecular descriptors must be used instead of inefficient morphological, physiological and biochemical characters to avoid ambiguities and to clearly define the inventor of a particular variety.

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.Keywords: DNA markers for rice, Rice marker haplotypes, Pleiotropic genes in rice, Rice breeding in Sri Lanka, SNP and INDEL in rice breeding.