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

Abstract

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.

Keywords: RILs; SNPs; introgression lines; linkage map; yield related traits.

FIGURE 1

Genotype distribution of SLAF markers. The Y axis represents the number of SLAFs, the X axis represents the type of SLAFs.

FIGURE 2

Phenotypic evaluation of PL for G1025, K1561, and RILs. The Y axis represents the number of plant individuals. The X axis is continuous for panicle length: 16 cm < PL ≤ 18 cm; 18 cm < PL ≤ 20 cm; 20 cm < PL ≤ 22 cm; 22 cm < PL ≤ 24 cm; 24 cm < PL ≤ 26 cm; 26 cm < PL ≤ 28 cm; 28 cm < PL ≤ 30 cm; PL > 30 cm.

FIGURE 3

Quantitative trait loci (QTL) analysis with panicle length (PL) using the high-density genetic map. (A) QTL analysis of PL in the early season of Nanning (NN) in 2014; (B) QTL analysis of PL in the late season of Nanning (NN) in 2014; (C) QTL analysis of PL in NN in 2015; (D) QTL analysis of PL in Wuhan (WH) in 2015. The horizontal line on the chart represents the LOD threshold.

FIGURE 4

Genetic linkage map with locations of QTLs on chromosomes 4, 9, and 10.

FIGURE 5

Genotypes and phenotypes of 13 RILs and parents. Left figure: genotypes of 13 RILs and parents; Mark-SLAF1-19, Marker839969, Marker775801, Marker868127, Marker823913, Marker891014, Marker803328, Marker860031, Marker768445, Marker797853, Marker860076, Marker871127, Marker775977, Marker824122, Marker864241, Marker876655, Marker911696, Marker866573, Marker891726, Marker864313, respectively. The solid bar represents segments of G1025, and the hollow bar represents segments of K1561. Right figure: phenotypes of 13 RILs and parents.