Abstract
Panicle length (PL) is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Three populations were used to identify QTLs and candidate genes associated with PL. Four QTLs for PL were detected on chromosomes 4, 6, and 9 through linkage mapping in the recombinant inbred line population derived from a cross between the cultivars Xiushui79 (short panicle) and C-bao (long panicle). Ten SSR markers associated with PL were detected on chromosomes 2, 3, 5, 6, 8, 9, and 10 in the natural population consisting of 540 accessions collected from East and Southeast Asia. A major locus on chromosome 9 with the largest effect was identified via both linkage and association mapping. LONG PANICLE 1 (LP1) locus was delimited to a 90-kb region of the long arm of chromosome 9 through fine mapping using a single segment segregating F2 population. Two single nucleotide polymorphisms (SNPs) leading to amino acid changes were detected in the third and fifth exons of LP1. LP1 encodes a Remorin_C-containing protein of unknown function with homologs in a variety of species. Sequencing analysis of LP1 in two parents and 103 rice accessions indicated that SNP1 is associated with panicle length. The LP1 allele of Xiushui79 leads to reduced panicle length, whereas the allele of C-bao relieves the suppression of panicle length. LP1 and the elite alleles can be used to improve panicle length in rice.
Highlights
Rice (Oryza sativa L.) is an important staple food that feeds approximately 50% of the world’s population
Previous studies have demonstrated that panicle length is a typical quantitative trait controlled by multiple genes and may be significantly influenced by environmental conditions (Yao et al, 2015)
The number and effect of QTLs for panicle length detected via linkage mapping may differ among segregating populations, such as F2 populations, recombinant inbred lines (RILs) or backcrossed inbred lines (Huang and Han, 2014), and these differences may underlie the identification of approximately 253 QTLs for panicle length distributed on 12 chromosomes (Xiao et al, 1998; Hittalmani et al, 2002, 2003; Xing et al, 2002; Kobayashi et al, 2003; Thomson et al, 2003; Ashikari et al, 2005; Lee et al, 2005; Mei et al, 2005; Cho et al, 2007; Liu et al, 2011; Marathi et al, 2012; Yao et al, FIGURE 5 | Phylogenetic analysis of the LONG PANICLE 1 (LP1) protein. (A) Phylogenetic tree of the LP1-like proteins in higher plants
Summary
Rice (Oryza sativa L.) is an important staple food that feeds approximately 50% of the world’s population. Rice is grown globally on approximately 160 million hectares annually and the average yield is 4.4 tons per hectare (GRiSP, 2013). Panicle length is one aspect of panicle architecture and is usually measured as a yield-related trait. Together with spikelet number and density, seed setting rate and grain plumpness, determines the grain number per panicle; yield increases in rice. Studies focusing on traits that are components of grain yield and quality, such as grain number, panicle number and grain weight, have revealed a few genes associated with these traits, such as GS3, GS5, GW2, GW5, GW8, Gn1, Candidate Gene Identification for PL
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