Fine mapping of a novel locus qIGL1 (INCREASE GRAIN LENGTH 1), a major QTL for modulating grain length in rice
Grain length is a prominent determinant for the grain weight and appearance quality of rice. To elucidate the genetic basis of the control of grain length, we conducted quantitative trait locus (QTL) mapping to determine a genomic interval responsible for the a long-grain phenotype observed in a japonica cultivar HD385 by using an F2:3 population and recombinant inbred line (RIL) population, which is are derived from a cross between the long-grain japonica cultivar HD385 and short-grain japonica cultivar Nipponbare (NIP). This led to the identification of a novel QTL, which is located on chromosome 3, for grain length, named qIGL1 (for Increased Grain Length 1); the HD385-derived allele showed enhancement effects on grain length, and such an allele as well as NIP-derived allele are were thus designated qigl1 HD385 and qIGL1NIP, respectively. Genetic analysis revealed that qigl1HD385 displayed semi-dominant effects on grain length. To further narrow down the qIGL1 region, we developed a few advanced backcross populations to determine the precise location of qIGL1. Eventually, qIGL1 was delimited to a 70.8-kb region containing 9 open reading frames (ORFs). A comprehensive analysis indicated that ORF6 and ORF9, separately corresponding to LOC_Os03g30530 and LOC_Os03g30550, are were found to carry base substitutions and/or deletions, which resulted in changes or losses of amino acid residues. However, these alterations in coding sequences does did not significantly change the expression levels of both ORFs. To further elucidate the mechanisms behind the increases of grain length conferred by qigl1HD385, we generated a pair of near-isogenic lines (NILs), termed NIL-qigl1HD385 and NIL-qIGL1NIP, and discovered that introduction of qigl1HD385 into the NIP background significantly lead resulted into the elevations of grain length and 1000-grain weight. Closer inspection of outer epidermal cells of grain surfaces of both lines revealed that the cell length and width in the longitudinal direction are were significantly longer in NIL-qigl1HD385 compared with in NIL-qIGL1NIP, which may might stem partly from the downregulation of several cell cycle-related genes. Hence, our study studies identify identified a new semi-dominant natural allele contributing to the increase of grain length, and further shed light on the regulatory mechanisms of grain length. Overall design: To further elucidate the mechanisms behind the increases of grain length conferred by qigl1HD385, we generated a pair of near-isogenic lines (NILs), termed NIL-qigl1HD385 and NIL-qIGL1NIP. We performed gene expression profiling analysis using data obtained from RNA-seq of 8-10 cm young panicle of NIL-qigl1HD385 and NIL-qIGL1NIP. Identify the differentially expressed genes (DEGs) between NIL-qigl1HD385 and NIL-qIGL1NIP by comparative gene expression profiling analysis of RNA-seq data for NIL-qigl1HD385 and NIL-qIGL1NIP.