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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS

Location: Dale Bumpers National Rice Research Center

Title: A major gene resistant to straighthead was identifed using two RIL populations

Authors
item Xuhao, Pan -
item Yan, Wengui
item JIA, MELISSA
item JACKSON, AARON
item Jia, Limeng -
item Qijun, Zhang -
item Pizhou, Xu -
item Bihu, Huang -
item Femando, Correa -
item Shigui, Li -

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: February 27, 2012
Publication Date: February 1, 2013
Citation: Xuhao, P., Yan, W., Jia, M.H., Jackson, A.K., Jia, L., Qijun, Z., Pizhou, X., Bihu, H., Femando, C., Shigui, L. 2013. A major gene resistant to straighthead was identifed using two RIL populations. Rice Technical Working Group Meeting Proceedings. Feb.27-Mar.1,2012. Hot Springs, AR. pg. 45.

Technical Abstract: Straighthead, a physiological disorder of rice (Oryza sativa) characterized by sterility of florets and an accompanying reduction in yield, occurs in numerous countries including the US. Cultivar resistance is the most effective and economical strategy for straighthead control. Understanding the genetic basis for straighthead resistance in rice sets a solid foundation for cultivar improvement. In this study, we developed two recombinant inbred line (RIL) F9 populations, Zhe733 (resistant)/R312 (susceptible) and Cocodrie (susceptible)/Jing185 (resistant). Straighthead was evaluated in single row plots in a randomized complete block design with three replications at Dale Bumpers National Rice Research Center in 2008 and the evaluation was repeated in 2009. Monosodium methyl arsenate (MSMA) at 6.7 kg ha-1 as a solution was applied to the soil surface and incorporated before planting in order to induce straighthead. The parents of each population were repeatedly tested in each tier as controls. Straighthead was rated using a scale of 1 to 9 at maturity based on floret fertility or sterility and panicle emergence from the flag leaf sheath, where 9 was the most susceptible and 1 was the most resistant. Means from 6 replications for each line gathered over a two year period were used for gene mapping. In total, 170 Zhe733/R312 F9 RILs and 91 Cocodrie/Jing185 F9 RILs were screened with 136 (selected from 521) and 159 (selected from 473) polymorphic markers, respectively. JoinMap 4.0 was used to calculate marker distance and build linkage maps for each population. Qgene 4.3.8 was used to estimate QTL parameters (locations, effects and test statistics) with composite interval mapping (CIM). QTL with logarithm of odds (LOD) scores > 3.0 were reported as QTL for straighthead resistance. Four loci were identified from the Zhe733/R312 population, one on Chromosome (Chr) 8 (LOD=23.0), Chr7 (LOD=5.0), Chr6 (LOD= 4.8) and Chr11 (LOD=3.0). From the Cocodrie/Jing185 population two loci were identified, one on Chr8 (LOD= 27.0) and another on Chr3 (LOD=3.8). The QTL region on Chr8 was the largest QTL identified in both populations. The Chr8 QTL explained 42% of total variation with a gene effect of -1.93 in Zhe733/R312 and 67% of total variation with a gene effect of -2.05 in Cocodrie/Jing185. Negative effect of the gene indicates a decrease of straighthead rating and increase of straighthead resistance. The QTL on Chr8 was located between RM6838 and RM72 within a genetic distance of 1.0 cM and a physical distance of 0.91 Mb in Zhe733/R312. The QTL region of Zhe733/R312 on Chr8 overlapped with the region identified from the Cocodrie/Jing185 population. The QTL region in Cocodrie/Jing185 was between RM22559 and RM72 with a genetic distance of 1.9 cM and a physical distance of 1.02 Mb. RM6838 in Zhe733/R312 and RM22559 in Cocodrie/Jing185 were physically located very close to each other at 5.85 Mb and 5.70 Mb, respectively. RM72 at 6.76 Mb was the most distal marker of the QTL identified in both populations. The overlapping intervals on Chr8 identified in both populations verify the presence of a major QTL at this location. Application of molecular markers to plant breeding is regarded as an efficient and economical way to evaluate or identify the trait of interest through genotype instead of phenotype, especially for straighthead which evaluation requires MSMA. Successful application of marker-assistant selection (MSA) depends on three factors: 1) marker(s) should co-segregate or be closely linked (genetic distant 1cM or less is sufficient for MAS) with the desired trait, 2) marker(s) should tightly linked to no more than three QTLs, and 3) all QTLs selected for MAS should be stable across environments. In the present study, straighthead evaluation was conducted over two years, which accounted for environmental effects. We are making further efforts to fine map this gene. Molecular marker(s) identified from fine mapping will be verified using straighthead information in the USDA rice core collection. Once verified, the markers associated with this QTL will be ready for breeders to use for cultivar improvement.

Last Modified: 8/19/2014
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