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

Zhengzheng Zhu,Yu Wei,Sibin Guo,Aihua Sha,Xiaoqiong Li

doi:10.3389/fpls.2018.01492

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.

Highlights

Rice is the most widely consumed staple food for a large part of the world’s human population, especially in Asia
K1561 is a long panicle variety developed from the backcross progenies of IR24 and O. minuta (Guo, 2009), and G1025 is a short panicle restorer line widely used in Guangxi Province of China
The average number of Specific Locus Amplified Fragment (SLAF) was 108,127 in the recombinant inbred line (RIL) population, and the coverage was an average of 5.95-fold (Table 1)

Summary

Introduction

Rice is the most widely consumed staple food for a large part of the world’s human population, especially in Asia. To meet consumption demand of the growing world population, high-yield variety breeding is one of the major targets for modern breeders. In China, rice yield has been greatly improved during past decades owing to breeding of dwarfism, utilization of hybrid vigor, and cultivation and extension of super rice varieties. The narrow genetic basis of the super rice varieties has currently limited further improvements of yield. These yield improvements will likely only be achieved by expanding the available genetic resources.

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