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.

Hybrid rice (Oryza sativa) has been cultivated commercially for 42 years in China. However, poor grain filling still limits the development of hybrid japonica rice. We report here the map-based cloning and characterization of the GRAIN-FILLING RATE1 (GFR1) gene present at a major-effect quantitative trait locus. We elucidated and confirmed the function of GFR1 via genetic complementation experiments and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPRassociated protein 9 (Cas9) gene editing in combination with genetic and molecular biological analyses. In addition, we conducted haplotype association analysis to mine the elite alleles of GFR1 among 117 rice accessions. We observed that GFR1 was constitutively expressed and encoded a membrane-localized protein. The allele of the rice accession Ludao (GFR1 Ludao) improved the grain-filling rate of rice by increasing Rubisco initial activity in the Calvin cycle. Moreover, the increased expression of the cell wall invertase gene OsCIN1 in the near isogenic line NIL-GFR1 Ludao promoted the unloading of Suc during the rice grain-filling stage. A yeast two-hybrid assay indicated that the Rubisco small subunit interacts with GFR1, possibly in the regulation of the rice grain-filling rate. Evaluation of the grain-filling rate and grain yield of F1 plants harboring GFR1 Ludao and the alleles of 20 hybrids widely cultivated commercially confirmed that favorable alleles of GFR1 can be used to further improve the grain-filling rate of hybrid japonica rice.

The panicle exsertion length (PEL) in rice (Oryza sativa L.) is an important trait for hybrid seed production. We investigated the PEL in a chromosome segment substitution line (CSSL) population consisting of 66 lines and a natural population composed of 540 varieties. In the CSSL population, a total of seven QTLs for PEL were detected across two environments. The percentage of phenotypic variance explained (PVE) ranged from 10.22 to 50.18%, and the additive effect ranged from −1.77 to 6.47 cm. Among the seven QTLs, qPEL10.2 had the largest PVE, 44.05 and 50.18%, with an additive effect of 5.91 and 6.47 cm in 2015 and in 2016, respectively. In the natural population, 13 SSR marker loci were detected that were associated with PEL in all four environments, with the PVE ranging from 1.20 to 6.26%. Among the 13 loci, 7 were novel. The RM5746-170 bp allele had the largest phenotypic effect (5.11 cm), and the typical carrier variety was Qiaobinghuang. An RM5620-RM6100 region harboring the EUI2 locus on chromosome 10 was detected in both populations. The sequencing results showed that the accessions with a shorter PEL contained the A base, while the accessions with a longer PEL contained the G base at the 1,475 bp location of the EUI2 gene.

No abstract