Quantitative trait loci (QTLs) for the starch-related traits amylose content (AC) and resistant starch (RS) content have received much attention due to the potential benefits of grains high in these starch levels. In this study, QTLs associated with AC and RS content were identified using 92 recombinant inbred lines (RILs) developed from a cross between two closely related japonica cultivars ‘Dodamssal’ and ‘Hwayeong’. One QTL on chromosome 2 for RS content and 2 QTLs for AC on chromosomes 2 and 6 were detected. The F₂ population derived from a cross between Hwayeong and two selected RILs were used to analyze the interaction between starch branching enzyme 3 (SBE3) and granule-bound starch synthase 1 (GBSS1). The combined effect of SBE3 and GBSS1 in the F₂ population suggested that these two genes behaved in an additive manner in increasing AC. Haplotype analysis based on two SNPs in GBSS1 classified 117 rice accessions into three groups. At the first SNP site, all indica, Korean landrace, and weedy rice accessions had the Wx^a allele at the 5ʹ splice site of intron 1, whereas japonica accessions had the mutated Wx^b allele. This suggests that this splice-donor mutation is prevalent in japonica cultivars, but rare or absent in landrace and weedy rice cultivars. Landrace or weedy rice accessions harboring the Wx^a allele could be employed in breeding programs to manipulate AC in cultivated japonica rice considering the difficulty and time to introduce desirable indica traits into japonica due to reproductive barriers.

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• Improved Processing Quality in a tongil-type Waxy Rice Cultivar Associated with a Rare granule-bound starch synthase I Allele
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• Evaluation of glycemic response and starch digestibility in Korean rice toward the development of low GI rice
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• Allelic Diversity at Protein Disulfide Isomerase Like 1-1 (PDIL1-1) Gene is Associated with Amylose Content in Japonica Rice
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• Quality Characteristics of Rice-Based Ice Creams with Different Amylose Contents
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  Frontiers in Plant Science.2022;[Epub]     CrossRef
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Salinity is a common and increasing problem in many coastal rice producing areas around the world. Salinity tolerance at the reproductive stage in rice is crucial as it determines grain yield. An F₂ mapping population was developed from two modern rice cultivars contrasting in tolerance: NSIC Rc222 (a high-yielding salt-sensitive variety released in the Philippines) and BRRI dhan 47 (a salt-tolerant variety released in Bangaldesh). The performance of the F₂ population showed transgressive segregation in the yield components under salinity stress of EC 10 dS/m under salinized field conditions. Ninety-six single nucleotide polymorphism (SNP) markers using 96-plex Fluidigm^TM genotyping were used to construct a linkage map of 1306.2 cM (Kosambi), with an average interval size of 13.6 cM. Seven putative quantitative trait loci (QTLs) for reproductive stage salinity tolerance traits having LOD values ranging from 2.9 to 4.1 were identified on chromosomes 1, 2, 5 and 11, explaining 13.4 to 18.4% of the phenotypic variation. Results of this mapping study identified a genomic region on chromosome 2 that confers salinity tolerance at the reproductive stage as measured by the number of filled spikelets, percent filled spikelets and yield. This study reports the molecular mapping of QTLs controlling reproductive-stage salinity tolerance-related traits, which will be useful in marker-assisted selection and breeding population development in rice.

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  Crop Science.2025;[Epub]     CrossRef
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  Journal of Plant Growth Regulation.2022; 41(6): 2347.     CrossRef
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  International Journal of Molecular Sciences.2022; 23(19): 11376.     CrossRef
• Identification of Quantitative Trait Loci Related to Salt Tolerance of Indica Rice RIL Population in Different Growth Stages
  S. M. M. Razi, R. Shirzadian-Khorramabad, H. Sabouri, B. Rabiei, H. H. Moghadam
  Russian Journal of Genetics.2022; 58(9): 1091.     CrossRef
• Genetic Mapping to Detect Stringent QTLs Using 1k-RiCA SNP Genotyping Platform from the New Landrace Associated with Salt Tolerance at the Seedling Stage in Rice
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• Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel
  Caijin Chen, Gareth J. Norton, Adam H. Price
  Frontiers in Plant Science.2020;[Epub]     CrossRef

Previously, we mapped the qSPP7 QTL affecting the number of spikelets per panicle (SPP) on rice chromosome 7 using near-isogenic line (NIL WH29001) derived from an interspecific cross between the japonica ‘Hwaseong’ and Oryza minuta. In the present study, we confirmed this QTL using progeny derived from a cross between IL102, a WH29001 sister line and Hwaseong. Genetic analysis determined that qSPP7 was located between a KASP marker KJ07–049 and RM21605. The O. minuta segment on chromosome 7 introgressed into the Hwaseong background was associated with an increase in SPP. The panicle structure of IL102 revealed that not only the number of SPP increased significantly, but also the number of branches per panicle increased as compared to Hwaseong suggesting that the donor allele of qSPP7 promotes branching in the genetic background of Hwaseong. Linkage analysis indicated that qEhd1 on chromosome 10 is involved in the difference in heading date of IL102 and Hwaseong. Experiments under 3 different day length conditions revealed that IL102 always showed earlier heading and higher SPP as compared to Hwaseong indicating that the effect of qSPP7 in the Hwaseong background was not dependent on photoperiod, and SPP increased in proportion to the number of days to heading.

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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.

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