No abstract

Phosphorous deficiency (PD) tolerance is a pivotal trait that is advantageous if present in modern day high performing rice varieties. However most of the frequently grown mega rice varieties lack this trait leading to expensive application of artificial phosphate fertilizer results secondary consequences such as environmental pollution and higher cost of production. Marker assisted breeding (MAB) for PD tolerance in rice is often hailed as the pragmatic solution to tackle this problem. The genetic basis of PD tolerance in rice has been dissected using a wide cross made between PD tolerant rice landrace Kasalath and a sensitive landrace Nipponbare. A major QTL known as Pup1 has been identified, molecularly characterized and underlying polymorphisms were detected. A major INDEL region within Pup1 QTL within Kasalath background is conferred to control the PD tolerance which is genetically 'null' in Nipponbare background. The DNA marker K46 which is present within Pup1 has been developed to identify this INDEL region in Kasalath like genotypes. The PD tolerance in Sri Lankan rice germplasm has been recently studied using a core panel of rice genotypes that are important in rice breeding programs. It is important to figure out the genomic landscape of the INDEL region of Pup1 QTL in these Sri Lankan rice genotypes. Therefore the present study was conducted to characterize the K46 DNA marker locus of the previously characterized for PD tolerance rice cultivars in Sri Lanka. The K46 specific primer-pair was assayed across 30 selected Sri Lankan cultivars and the PCR products were sequenced. The resulted DNA sequences were aligned with the Kasalath reference sequence for K46 locus. Further cluster analysis of the identified SNPs resulted four distinct haplotypes in which nine cultivars were grouped with Kasalath like haplotype, two unique haplotypes and the null haplotype. However, there is no strong association between the haploype class and the PD tolerance score of the cultivars implying the potentially novel PD tolerance mechanisms that require further studies.

Pup1 is the major quantitative trait locus (QTL) for phosphorus deficiency (PD) tolerance in rice. The molecular markers linked to Pup1 are available for numerous rice genotypes. However, novel haplotypes of Pup1 could be detected if specific landraces are subjected to genetic analyses. A set of 30 local rice genotypes were assessed for PD tolerance and in the present study, they were characterised by sequencing K20-1, a co-dominant locus within the Pup1 locus. The DNA polymorphism was also checked for the association with PD tolerance. A total of 10 SNPs and one INDEL were discovered among the 32 genotypes including Kasalath and Nipponbare as PD tolerant and sensitive reference rice varieties, respectively. Four unique SNPs were discovered in the studied germplasm that are not present in either Kasalath or Nipponbare. The SNP located at the 209 th position was very important as it is unique to highly PD tolerant landraces Murungakayan and Suduheenati, and varieties H-4, H-7 and H-10. These five genotypes lack the INDEL region present in Kasalath highlighting the presence of novel Pup1 haplotypes in country specific rice varieties/ landraces, and they can be used as parental genotypes to introduce PD tolerance into new varieties in rice breeding programmes in Sri Lanka.

Pup1 varietiestolerant cultivars is important for rice farming. The DNA markers linked to Pup1 rice cultivars Kasalath and Nipponbare cannot be directly employed in regional breeding programmes contain diverse QTL haplotypes complicating marker assisted Pup1 linked DNA marker haplotypes present in local cultivars is the prerequisite this study was to identify the Pup1 haplotypes from a panel of 30 rice cultivars important for breeding programmes in Sri Lanka. A total of 17 Pup1 linked DNA markers were used to genotype the rice cultivars previously characterised for PD tolerance in comparison to Kasalath and Nipponbare. Overall 28 Pup1 haplotypes clustergram and the Pup1 hapoltype in Kasalath was observed in four PD tolerant cultivars Sudubalawee Kaluheenati and Marss Murungakayan contain haplotypes that are clustered separately from Kasalath indicating the possibility of conferring PD tolerance in the absence of Kasalath haplotype. The marker-trait association analysis for the PD tolerance revealed that selection of the favourable alleles such as 433 bp allele of K46-K2 marker could increase PD tolerance by 0.73.The detected positively associated alleles with PD tolerance can be readily employed in MAB of rice in Sri Lanka.

Phosphorous deficiency (PD) tolerance is a polygenic trait. The underlying genetics of PD tolerance trait is important to provide the basis for detecting Quantitative Trait Loci (QTLs) and validating markers that could be used in Marker Assisted Breeding (MAB) in rice. The PD tolerance of Sri Lankan rice germplasm has been characterized. However, no attempts were taken to develop and validate the DNA markers for the breeding purposes and to understand the genetic basis of the traits. The present research project was conducted to assess the PD related traits and to validate internationally published DNA markers that are linked to PD tolerance using Sri Lankan rice cultivars. A total of 84 crosses were made and advanced to F 2 and higher generations. Out of these crosses, an important subset of three crosses was selected based on the overall PD tolerance and sensitivity, importance as mega production varieties and pedigree connections between the cultivars. The plant height, number of tillers, shoot dry weight, leaf width, flag leaf width and the color metrics L*, a*, b*, hue (h*) and chroma (C*) were measured from 200 individuals each from the three populations grown under P deficient (P o) soil conditions. Except color traits, other traits were normally distributed and exhibited higher broad sensitivity. The color metrics indicate the presence of possible epistatic interactions between the major underlying loci. From each population, two extreme bulks were selected from the highest and lowest ends of shoot dry weight (SDW) for bulk segregant analyses (BSA) to validate the DNA markers for PD tolerance. It was observed that, DNA marker K46-K1 can be used for MAB of rice for PD tolerance. The genetic information generated in the present study can also be used for larger scale genomic studies such as SNPs, GBS and GWAS mapping.