Rice culm is an important trait for determining rice lodging yield, and stem diameter has been suggested as a yield-related trait; however, studies for the genetic basis of its phenotypic variation are still required. In this study, we used 160 recombination inbred lines derived from a cross of two different rice varieties [‘Milyang23’ (Tongil rice) and ‘Giho’ (japonica)] for quantitative trait locus (QTL) mapping with nine stem traits. The analysis showed that QTLs for the diameters of the first, second, third and fourth internode traits were independently separated in the top of chromosome 1, whereas four lengths of internodes were estimated as being related to the semidwarf1 (sd1) gene. A major-effect QTL (q2ID1) was identified that the overlapped region of our previous mapping with a large genomic region. Therefore, we performed high-resolution genetic mapping for fine-mapping of q2ID1 to a ~140 kb region between Ind1_1 and Ind1_2 of genetic markers, with candidate genes predicted using a reference genome. We ultimately identified nine of the 15 candidate genes with specific gene functions and analyzed the sequence variations between two parents. These results offer valuable gene and/or genetic information on stem diameter to improve lodging resistance and yield.

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• Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice (Oryza sativa L.)
  Ognigamal Sowadan, Shanbin Xu, Yulong Li, Everlyne Mmbone Muleke, Hélder Manuel Sitoe, Xiaojing Dang, Jianhua Jiang, Hui Dong, Delin Hong
  Genes.2024; 15(1): 105.     CrossRef

Functional stay-green (FSG) delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green (NFSG) retains only leaf greenness without sustaining photosynthetic activity. Retention of chlorophylls and photosynthetic capacity is important for increasing crop yield. We determined the main-effect quantitative trait loci (QTLs) for FSG traits in the japonica rice SNU-SG1 and isolated candidate genes. To identify QTLs influencing FSG, we analyzed eight traits: (1) 1 day after heading-degree of chlorophyll content of flag leaf, (2) 1 day after heading-degree of chlorophyll content of second leaf, (3) 1 day after heading-degree of chlorophyll content of flag and second leaves, (4) 50 day after heading-degree of chlorophyll content of flag leaf, (5) 50 day after heading-degree of chlorophyll content of second leaf, (6) 50 day after heading-degree of chlorophyll content of flag and second leaves, (7) relative decline degree of chlorophyll content of flag and second leaves, and (8) flowering time. We carried out QTL analysis with F₇ RIL from a cross of japonica rice ‘SNU-SG1’ and indica rice ‘Milyang23 (M23)’. Using 131 molecular markers, we identified 18 QTLs for the eight traits with a threshold LOD value > 2.8. Sequence analysis identified 16 candidate genes for 10 main-effect QTLs. Of these, we have chosen seven strong candidate genes for the 10 main-effect QTLs. These genetic resources will be useful for breeding high-yielding rice cultivars.

Citations

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  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Genetic analysis of stay‐green, yield, and agronomic traits in spring wheat
  J. P. Cook, R. K. Acharya, J. M. Martin, N. K. Blake, I. J. Khan, H.‐Y. Heo, K. D. Kephart, J. Eckhoff, L. E. Talbert, J. D. Sherman
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