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Wild rice possesses a large number of valuable genes that have been lost or do not exist in cultivated rice. To exploit the desirable gene controlling panicle length (PL) in wild rice  Oryza minuta , a recombinant inbred line (RIL) population was constructed that was derived from a cross between the long panicle introgression line K1561 with  Oryza minuta  segments and a short panicle accession G1025. Specific Locus Amplified Fragment (SLAF) sequencing technology was used to uncover single nucleotide polymorphisms (SNPs) and construct the high-density genetic linkage map. Using 201 RIL populations, a high-density genetic map was developed, and spanned 2781.76 cM with an average genetic distance 0.45 cM. The genetic map was composed of 5, 521 markers on 12 chromosomes. Based on this high-density genome map, quantitative trait loci (QTL) for PL were analyzed for 2 years under four environments. Seven QTLs were detected, which were distributed within chromosomes 4, 9, and 10, respectively.  pl4.1  was detected twice, and  pl10.1  was only detected once. Although  pl9.1  was only detected once, it was very near  pl9.2  in the genetic map which was detected three times. Thus, we speculate one major QTL exists in the region of  pl9.1  and  pl9.2  to control PL (temporarily referred to as  pl9 ).  pl9  is a potentially novel allele derived from  Oryza minuta , and it can be used for genetic improvement of cultivar rice.

frontiers in plant science

Identification of a Novel QTL for Panicle Length From Wild Rice (Oryza minuta) by Specific Locus Amplified Fragment Sequencing and High Density Genetic Mapping