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

High-throughput molecular markers with high genotyping accuracy will be helpful for genetic analysis, mapping of interesting genes, and rice breeding program. To develop high-throughput and cost-effective molecular markers for Korean japonica rice varieties, which are closely-related genetically, we designed kompetitive allele-specific polymerase chain reaction (KASP) assays from the sequence data of 13 Korean japonica rice varieties. Of the 504 new KASP assays, 371 (73.6%) showed polymorphisms among the tested varieties. In addition to the 400 previously developed KASP markers, this resulted in 771 KASP markers being applicable for Korean japonica rice varieties. These KASP markers were used to map the quantitative trait loci (QTLs) for rice bakanae disease (BD) resistance. From the results of QTL mapping and determination of the mortality rate of BD in two F²:F³ populations, a major QTL, qFfR1-1, and a novel QTL, qFfR6, were revealed on chromosome 1 in the Junam/Nampyeong F²:F³ population and on chromosome 6 in the Saenuri/Nampyeong F²:F³ population, respectively. Further, the insertion/deletion markers in the qFfR1-1 region were developed to select BD-resistant japonica rice varieties. The 771 developed KASP markers will accelerate the molecular breeding in Korean japonica rice varieties, and the detected QTLs will be helpful in identifying candidate genes for BD resistance.

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• Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties
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Closely-related cultivars generally used for crossing in breeding lack sufficient known DNA polymorphisms with already developed DNA markers even though they exhibit remarkable phenotype difference. However, next-generation sequencing (NGS) enables the identification of massive DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. This study conducted a whole-genome re-sequencing of two Korean japonica rice varieties, Junam and Nampyeong. The sequencing yielded 16.6 × 10⁹ bps for Junam, and 15.1 × 10⁹ bps for Nampyeong. After quality trimming and read mapping onto the reference genome sequence of Nipponbare, 11.9 × 10⁹ bps from Junam and 10.6 × 10⁹ bps from Nampyeong were mapped onto the reference sequence. The final effective mapping depth was 31.98x for Junam and 28.41x for Nampyeong. This study found 398,123 DNA polymophisms between Junam and Nampyeong. These were classified into 352,478 SNPs (88.5%) and 45,645 InDels (11.5%) by polymorphism types, 338,485 homozygous (85%) and 59,638 (15%) heterozygous by zygosity, and 331,855 intergenic (83.4%) and 66,268 genic (16.6%) by genomic location. To see the availability of these results in DNA marker development, Cleaved Amplified Polymorphic Sequences (CAPS) markers were developed based on 22 SNPs lying in restriction enzyme sites. Among them, 17 CAPS markers showed polymorphisms between Junam and Nampyeong. It is expected that sufficient DNA markers for mapping genes/QTLs with progeny population from a cross between Junam and Nampyeong can be developed based on the results of the study.

Citations

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• Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties
  Kyeong-Seong Cheon, Young-Min Jeong, Hyoja Oh, Jun Oh, Do-Yu Kang, Nyunhee Kim, Eungyeong Lee, Jeongho Baek, Song Lim Kim, Inchan Choi, In Sun Yoon, Kyung-Hwan Kim, Yong Jae Won, Young-il Cho, Jung-Heon Han, Hyeonso Ji
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• QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing
  Kyeong-Seong Cheon, Yong Jae Won, Young-Min Jeong, Youn-Young Lee, Do-Yu Kang, Jun Oh, Hyoja Oh, Song Lim Kim, Nyunhee Kim, Eungyeong Lee, In Sun Yoon, Inchan Choi, Jeongho Baek, Kyung-Hwan Kim, Hyun-Su Park, Hyeonso Ji
  Molecular Genetics and Genomics.2020; 295(5): 1129.     CrossRef
• Kompetitive Allele-Specific PCR Marker Development and Quantitative Trait Locus Mapping for Bakanae Disease Resistance in Korean Japonica Rice Varieties
  Kyeong-Seong Cheon, Young-Min Jeong, Youn-Young Lee, Jun Oh, Do-Yu Kang, Hyoja Oh, Song Lim Kim, Nyunhee Kim, Eungyeong Lee, Jeongho Baek, Inchan Choi, Kyung-Hwan Kim, Yong Jae Won, In Sun Yoon, Young-il Cho, Jung-Heon Han, Hyeonso Ji
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• Mapping of a major quantitative trait locus for bakanae disease resistance in rice by genome resequencing
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• Single Nucleotide Polymorphism (SNP) Discovery and Kompetitive Allele-Specific PCR (KASP) Marker Development with Korean Japonica Rice Varieties
  Kyeong-Seong Cheon, Jeongho Baek, Young-il Cho, Young-Min Jeong, Youn-Young Lee, Jun Oh, Yong Jae Won, Do-Yu Kang, Hyoja Oh, Song Lim Kim, Inchan Choi, In Sun Yoon, Kyung-Hwan Kim, Jung-Heon Han, Hyeonso Ji
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