Genotypic and phenotypic relatedness of a farmer-discovered variant with high-yielding rice growing in the same field

Abstract

Haridhan rice was discovered by a farmer in his field which was planted with the widely cultivated mega-rice BR11. He noticed Haridhan’s variant characters compared to BR11, saved the seeds, planted it in 4–5 successive generations and noted the increase in yield with low input in fertilizer. Due to the overall similarity between BR11 and Haridhan, breeders were unwilling to call the latter a different genotype. This study was therefore performed to investigate the genetic similarity between BR11 and Haridhan. Polymorphism between Haridhan and BR11 using 115 SSR markers was 25 %, close to the reported 11 % for essentially derived (EDV) maize inbred lines. Similarly, 40 RAPD and 1,536 SNP markers showed polymorphism to be 16 % and 5 %, respectively. SSR polymorphic loci between the two were absent in chr 4, 6 and 9 but present in variable numbers in the rest. Some of the embedded and highly polymorphic SSRs were found in the 5′UTR of regulatory genes like Ser–Thr protein kinase and evolutionarily conserved C-terminal protein and revealed a common motif for binding TRA2-BETA1, a Serine–Arginine-rich protein involved in regulating and selecting splice sites. Genetic distance based on the Dice coefficient between Haridhan and BR11 as well as the cultivars, Lal Swarna and Guti Swarna planted in neighboring fields is 0.24, 0.26 and 0.20, respectively, compared to an average of 0.03 for EDV’s like maize inbred lines. Therefore, Haridhan could possibly have been derived from a cross of BR11 with another BR11 having outcrossed genes from the rice cultivars Lal Swarna and Guti Swarna.