OsSYL2^AA, an allele identified by gene‐based association, increases style length in rice (Oryza sativa L.)

Abstract

Stigma characteristics are important factors affecting the seed yield of hybrid rice per unit area. Natural variation of stigma characteristics has been reported in rice, but the genetic basis for this variation is largely unknown. We performed a genome-wide association study on three stigma characteristics in six environments using 1.3 million single-nucleotide polymorphism (SNPs) characterized in 353 diverse accessions of Oryza sativa. An abundance of phenotypic variation was present in the three stigma characteristics of these collections. We identified four significant SNPs associated with stigma length, 20 SNPs with style length (SYL), and 17 SNPs with the sum of stigma and style length, which were detected repeatedly in more than four environments. Of these SNPs, 28 were novel. We identified two causal gene loci for SYL, OsSYL3 and OsSYL2; OsSYL3 was co-localized with the grain size gene GS3. The SYL of accessions carrying allele OsSY-L3 AA was significantly longer than that of those carrying allele OsSYL3 CC. We also demonstrated that the outcrossing rate of female parents carrying allele OsSYL2 AA increased by 5.71% compared with that of the isogenic line carrying allele OsSYL2 CC in an F 1 hybrid seed production field. The allele frequencies of OsSY-L3 AA and OsSYL2 AA decreased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement in stigma characteristics of parents of hybrid rice.

A Novel Embryo Phenotype Associated With Interspecific Hybrid Weakness in Rice Is Controlled by the MADS-Domain Transcription Factor OsMADS8

“…We investigated the stigma characteristics of these three accessions. W1944 had longer stigmas than HY and CR6078, which is consistent with the finding that eight accessions of O. rufipogon and four of O. nivara had CC alleles at OsSYL2 and OsSYL3 , contributing to an increase in the stigma length in these wild Oryza species ( Dang et al, 2020 ). Histological analysis of thin sections from these CR6078 embryos showed a cleavage between the coleoptile and epidermis without any tissue covering the coleoptile ( Figure 1E ).…”

SYL3-k increases style length and yield of F1 seeds via enhancement of endogenous GA4 content in Oryza sativa L. pistils

“…In rice, the stigma characteristics, a complex quantitative trait, are controlled by multiple genes with minor phenotypic effects (Uga et al 2003 , 2010 ; Yu et al 2003 ). To the best of our knowledge, 37 quantitative trait loci (QTLs) have been detected for the STL and they are distributed on all the 12 chromosomes (Uga et al 2003 , 2010 ; Yan et al 2009 ; Li et al 2010 ; Marathi et al 2015 ; Dang et al 2016 , 2020 ). Uga et al ( 2003 ) reported that the QTL qSTL-4 on the chromosome 4 has the largest additive effect, and the allele from accession W1944 can increase the STL by 0.106 mm compared with Pei-kul.…”

“…Uga et al ( 2003 ) reported that the QTL qSTL-4 on the chromosome 4 has the largest additive effect, and the allele from accession W1944 can increase the STL by 0.106 mm compared with Pei-kul. Thirty-nine QTLs have been identified for the SYL and they are located on chromosomes 1, 2, 3, 4, 6, 7, 9, 10, and 11 (Uga et al 2003 , 2010 ; Li et al 2010 ; Marathi et al 2015 ; Dang et al 2016 , 2020 ; Zhou et al 2017 ). Uga et al ( 2010 ) also reported that the QTL qSYL-3 on the chromosome 3 has the largest additive effect, and the allele from IR64 can increase the SYL by 0.102 mm compared with Kinandang Patong.…”

“…Uga et al ( 2010 ) also reported that the QTL qSYL-3 on the chromosome 3 has the largest additive effect, and the allele from IR64 can increase the SYL by 0.102 mm compared with Kinandang Patong. Finally, 30 QTLs have been identified for the TSSL and they are distributed on chromosomes 1, 2, 3, 4, 6, 7, 9, and 12 (Li et al 2010 ; Liu et al 2015a ; Marathi et al 2015 ; Dang et al 2016 , 2020 ). The percentages of phenotypic variance explained by these QTLs for TSSL range from 2.9 to 20.0%.…”

“…Among all these QTLs, one candidate gene, LOC_Os03g14850 (originally named qSTL3 ), has been identified for controlling TSSL (Liu et al 2015b ). Two genes, OsSYL2 and OsSYL3 , were identified for controlling the SYL (Dang et al 2020 ). However, the underlying mechanism of action of these genes is still unclear.…”