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.
Highlights
Since green revolution, profitable rice farming is believed to be entirely dependent on the application of artificial fertilizer
A total of six single nucleotide polymorphisms (SNPs) were detected at the 47th, 225th, 226th, 247th, 339th and 420th positions along the 523 bp region, indicating the overall degree of polymorphism was 1.15 %
When the overall score of Phosphorous deficiency (PD) tolerance of the cultivars was compared with the K46 haplotype, it was found that, PD tolerance score of the cultivars were not significantly associated with the K46 haplotypes (Table 1; p < 0.05)
Summary
Profitable rice farming is believed to be entirely dependent on the application of artificial fertilizer. Currently it is believed that the application of fertilizer itself cannot increase the rice production due to many reasons such as fixing nutrients by the soil systems and higher cost associated with the fertilizer inputs (Arai and Sparks, 2007). Prolonged and handful applications of fertilizer could dramatically pollute the environment (Cordell et al, 2009) and contribute to the health hazards (Chandrajith et al, 2010). Most of the rice growing soils lack the optimum levels of P for growth and development of rice (Fairhurst et al, 1999). Because of these reasons farmers tend to apply more P fertilizer, but they pollute the environment and increase the cost of production. An alternative strategy to overcome the P fertilizer led crisis is required
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