| Rice(Oryza L.)is an important staple crop consumed by global population.However,the current pace of yield increase for rice is insufficient to meet the demands from the rapidly growing population.Under this background,increasing yield is still an important issue for China’s food security.At the same time,with the change of consumption structure and the demand of supply-side reform in the new period,how to increase grain yield and improve grain quality has become the new target of rice breeding.At present,traditional breeding has shown great limitations in the breeding of elite varieties.Fortunately,molecular design breeding for rice varieties with higher yield potential and excellent grain quality offers opportunity to achieve such a breakthrough,but the most crucial requirement is to identify subset of genes/QTL that control grain yield and quality-related traits and illustrate the interactions and genetic effects among these genes/QTL.Therefore,the exploration of superior alleles related to yield and quality traits is of great practical significance for the increase and quality of rice in China.Rice yield and quality traits are comprehensive and complex traits,which are affected by multiple genetic and environmental factors.Studies have shown that traits related to panicle architecture and heading date are highly associated with yield and quality.In this stuy,QTL mapping was carried out for panicle architecture related traits and heading date by using a set of chromosomal segment substitution lines(CSSL)derived from the cross between the japonica cultivar Nipponbare(NP)and the indica cultivar 9311.Subsequencely,qPL5 and qHd2-1 were fine mapped based on the progeny test of the substitution lines that derived from the backcross overlapped populations and the candidate genes of qPL5 and qHd2-1 were also predicted.In additional,the genetic effects of qPL5 and qHd2-1 were also detailed analyzed.The specific results are as follows:(1)Based on the results of QTL mapping,qPL5 is a stably inherited QTL for PL.In order to define the localization of qPL5,line N58 encompassing 9311 allelic qPL5 was employed to construct the genetic analysis population.The results showed that the 9311 allele of qPL5 is partially dominant to that of the NP allele.Similarly,a set of introgression lines derived from backcross progeny of line N5 8 and NP were constructed.Based on the phenotyped of these lines,the qPL5 locus was finely mapped to a 21.86 kb genomic region with two candidate genes.One,LOC Os05g41230,encodes a BRI1-associated receptor kinase 1 and the other,LOC Os05g41240,encodes a myb-like DNA-binding domain containing protein.Through sequence comparison of the two genes in line N58/9311 and Nipponbare,a number of sequence polymorphisms were found in the promoter region and/or the CDS region.However,among of them only two SNPs in LOC_Os05g41230 can lead to amino acid change.Meanwhile,the results of qRT-PCR indicated that only LOC_Os05g41230 relative expression showed much higher in N58 than that in NP during in the young panicles of different developmental stages.Taken together,we thus proposed that LOC_Os05g41230 might as the candidate gene for qPL5.Furthermore,the genetic effect of qPL5 has been detailed illustrated based on phenotyped of two pairs of NIL under curved-panicle japonica variety NP background and erect-paniclejaponica variety Wuyujing3(WY3)background,respectively.Whether it is NP background or WY3 background,NIL carrying 9311-typeqPL5 showed no significant changes in agronomic trait except slight change in plant height and drastic changes in grain yield-related traits:this line had longer panicle and branch,more secondary branch number and grain number per panicle compared with check variety.Further analysis showed that the increased panicle length of NIL is due to an increased cell length of the panicle axis.(2)In this study,we characterized qHd2-1,a minor-effect QTL for promoting heading date(by 3-4 days)under long-day condition(LD),but not short-day condition qHd2-1 was detected in a single segment substitution line N22-1,which was developed using indica 9311 as the donor,and japonica Nipponbare(NP)as the recipient.A set of substitution lines were developed from a segregating population derived from a cross between N22-1 and NP.Based on the genotypic identification and phenotypic evaluation of the target substitution lines,qHd2-1 was precisely located to an interval of～105 kb delineated by molecular markers STS2-20 and STS2-22 on an introgressed segment of chromosome 2.There are 17 ORFs in the positioning interval,4 of whichhave clear functional annotations,namely LOC_Os02g01355,LOC_Os02g01360,LOC_Os02g01440 and LOC_Os02g01480.Further analysis showed that LOC_Os02g01355 and LOC_Os02g01360 are MADS-box genes.It has been clearly reported that the MADS-box gene is involved in the genetic regulation of the heading date.Sequence comparison showed that both LOC_Os02g01355 and LOC_Os02g01360 exist some base variations in the promoter region.Conversely,only LOC_Os02g01355 exist base variations in the CDS region.Importantly,the expression level of LOC_Os02g01360 in line N22-1 was higher than that of NP and showed circadian rhythm changes under long-day conditions.This result is consistent with the phenotype of the earlier heading date of N22-1.Taken toghter,we speculated that LOC_Os02g01360 may be the candidate gene for qHd2-1.Additionally,qHd2-1 was found to function by up-regulating the florigen genes Hd3a and RFT1 during floral induction under LDs.A near-isogenic line containing a 560 kb donor fragment was constructed under the background of Nipponbare.It was clarified that qHd2-1 promotion of heading date affects grain yield-related agronomic traits,such as plant height,tiller number,and flag leaf size,as well as thousand-grain weight and grain width.The proportions are 11.05%,14.4%,10.86%and 8.29%,respectively.In conclusion,these findings not only establish a foundation for cloningqPL5 and qHd2-1,but also provide genetic resources for molecular design of high-yield and high-quality rice varieties. |
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