Dataset Information

Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.).

ABSTRACT: The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4?cM and covering 12 rice chromosomes with an average interval of 9.6?cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS) were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1?Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning.

SUBMITTER: Lee GH

PROVIDER: S-EPMC4933857 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.).

Lee Gyu-Ho GH Kang In-Kyu IK Kim Kyung-Min KM

International journal of genomics 20160622

The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interv ...[more]

PMID: 27419124

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Project description:Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica), grown under normal nitrogen and low nitrogen cultivation open field conditions. The results of the phenotypic evaluation indicated that parental lines 93-11 (P1, a high tillering indica cultivar) and Milyang352 (P2, a low tillering japonica cultivar) showed distinctive phenotypic responses, also reflected in their derived population. In addition, the linkage mapping and quantitative trait locus (QTL) analysis detected three QTLs associated with tiller number on chromosome 2 (qTNN2-1, 130 cM, logarithm of the odds (LOD) 4.14, PVE 14.5%; and qTNL2-1, 134 cM, LOD: 6.05, PVE: 20.5%) and chromosome 4 (qTN4-1, 134 cM, LOD 3.92, PVE 14.5%), with qTNL2-1 having the highest phenotypic variation explained, and the only QTL associated with tiller number under low nitrogen cultivation conditions, using Kompetitive Allele-Specific PCR (KASP) and Fluidigm markers. The additive effect (1.81) of qTNL2-1 indicates that the allele from 93-11 (P1) contributed to the observed phenotypic variation for tiller number under low nitrogen cultivation. The breakthrough is that the majority of the candidate genes harbored by the QTLs qTNL2-1 and qTNN4-1 (here associated with the control of shoot branching under low and normal nitrogen cultivation, respectively), were also proposed to be involved in plant stress signaling or response mechanisms, with regard to their annotations and previous reports. Therefore, put together, these results would suggest that a possible crosstalk exists between the control of plant growth and development and the stress response in rice.

Project description:Background:Grain weight is a grain yield component, which is an integrated index of grain length, width and thickness. They are controlled by a large number of quantitative trait loci (QTLs). Besides major QTLs, minor QTLs play an essential role. In our previous studies, QTL analysis for grain length and width was performed using a recombinant inbred line population derived from rice cross TQ/IRBB lines. Two major QTLs were detected, which were located in proximity to GS3 and GW5 that have been cloned. In the present study, QTLs for grain weight and shape were identified using rice populations that were homozygous at GS3 and GW5. Method:Nine populations derived from the indica rice cross TQ/IRBB52 were used. An F10:11population named W1, consisting of 250 families and covering 16 segregating regions, was developed from one residual heterozygote (RH) in the F7generation of Teqing/IRBB52. Three near isogenic line (NIL)-F2 populations, ZH1, ZH2 and ZH3 that comprised 205, 239 and 234 plants, respectively, were derived from three RHs in F10:11. They segregated the target QTL region in an isogenic background. Two NIL populations, HY2 and HY3, were respectively produced from homozygous progeny of the ZH2 and ZH3 populations. Three other NIL-F2 populations, Z1, Z2 and Z3, were established using three RHs having smaller heterozygous segments. QTL analysis for 1000-grain weight (TGW), grain length (GL), grain width (GW), and length/width ratio (LWR) was conducted using QTL IciMapping and SAS procedure with GLM model. Result:A total of 27 QTLs distributed on 12 chromosomes were identified. One QTL cluster, qTGW2/qGL2/qGW2 located in the terminal region of chromosome 2, were selected for further analysis. Two linked QTLs were separated in region Tw31911-RM266. qGL2 was located in Tw31911-Tw32437 and mainly controlled GL and GW. The effects were larger on GL than on GW and the allelic directions were opposite. qTGW2 was located in Tw35293-RM266 and affected TGW, GL and GW with the same allelic direction. Finally, qTGW2 was delimited within a 103-kb region flanked by Tw35293 and Tw35395. Conclusion:qTGW2 with significant effects on TGW, GL and GW was validated and fine-mapped using NIL and NIL-F2 populations. These results provide a basis for map-based cloning of qTGW2 and utilization of qTGW2 in the breeding of high-yielding rice varieties.

Dataset Information

Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.).

Publications

Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.).

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