A total of 857 rice breed lines were used to evaluate rice blast resistance. Frequency of leaf spot index was skewed to the right of the 1-9 scale in bar plot, with a score of 7 showing the highest frequency. The average spot index score of 857 breed lines was 5.33. Associations showing higher than the threshold of ‒log10(P) = 5.17 were detected as significant associations. Significantly associated single nucleotide polymorphism (SNP) markers located within ± 250 kb on the lead SNP position was designated to one QTL locus of lead SNP markers. Five association loci were detected. Two associated QTLs detected on Chr. 4 were designated as qRB4.1 and qRB422, explaining 17.8% and 14.3% of total phenotypic variations, respectively. Associated QTLs detected on Chr. 1, 11, and 12 (one each) designated as qRB1, qRB11 and qRB12 explained 44.6%, 9.09%, and 13.7% of total phenotypic variations, respectively. We compared previously reported QTLs. The location of qRB4.2 was overlapped with the previously reported QTL for blast field resistance. The location of qRB12 was also overlapped with the field resistance leaf blast. The other one, qRB4.1, was overlapped with bacterial blight resistance.

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• Genome-Wide Association Study of Body Conformation Traits in Tashi Goats (Capra hircus)
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• Genome-Wide Association Study of Submergence Tolerance in Rice (Oryza sativa L.)
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Bakanae disease is an important fungal disease caused by Gibberella fujikuroi. The outbreak of rice bakanae disease causes the most important problems for rice producing countries and affects almost all known rice cultivars. Identifying balance disease resistance in Korean Rice Landrace with diverse genetic sources is important for efficient breeding. In this study, we tried to find out useful genetic resources for bakanae resistant cultivar. The result suggested highly strong 3 varieties (‘IT010631’, ‘IT009118’ and ‘IT009221’.) to be used in breeding program. Additionally, we applied reported marker related qFfR1 bakanae disease to accessions which showed strong resistance. It is expected that these resources can be used to develop useful cultivars for each trait. Especially, accessions showed strong resistance in this study have different genotype with reported resistant resources, they would be used to find other genes related to bakanae resistance.

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• Current insights on rice (Oryza sativa L.) bakanae disease and exploration of its management strategies
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Rice is a temperature-sensitive crop, its yield is severely affected by low temperature, especially cold stress at the seedling stage will delay heading. To understand the genetic basis of cold tolerance, we evaluated the cold tolerance at the seedling stage of 136 rice accessions. To evaluate cold tolerance, we treated rice seedlings with cold water irrigation for ten days and scored the cold tolerance on a 1-9 scale, based on their low-temperature response and subsequent recovery. The genome-wide association study for cold tolerance revealed seven QTLs on chromosomes 1, 3, 6, 7, 10, and 12. The genomic region of the qCWS7 on chromosome 7 overlapped with a previously reported QTL associated with cold tolerance in the germinating stage. Similarly, qCWS1-1, qCWS1-2, qCWS3, qCWS6, and qCWS10 overlapped with a previously reported QTL associated with drought-stress tolerance. Subsequent bioinformatic and haplotype analyses suggested that five candidate genes affect cold tolerance: Os01g0228600 encoding a cytosolic hydroxypyruvate reductase, Os03g0115000 encoding a cupredoxin domain containing protein, Os06g0612800 encoding a stress-associated protein (SAP) gene family, Os12g0552500 encoding a universal stress protein (USP), and Os10g0482900 encoding a thioredoxin fold domain containing protein.

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• Genome-wide Association Study for Cold Tolerance at Seedling Stage Using a Core Collection of Korean Rice
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• Predicting the influence of extreme temperatures on grain production in the Middle-Lower Yangtze Plains using a spatially-aware deep learning model
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At the reproductive development stage of rice (Oryza sativa L.), temperature stress can decrease spikelet fertility, ultimately resulting in a yield loss. In this study, a total of 98 rice varieties were used in genome-wide association study (GWAS) to understand spikelet fertility under a high temperature (SFHT). GWAS results revealed that two lead SNPs were significantly associated with SFHT. Candidate genes located within ± 250 kb of the corresponding SNP position were discovered, resulting in a total of 21 candidate genes on chromosome 10 and 18 candidate genes on chromosome 11. Based on previously reported function and haplotype analysis, Os10g0177200 (EF-HAND 2domain containing protein) as one candidate gene showed significant differences among groups of haplotypes. This candidate gene will be further evaluated for its function to determine whether it is useful for improving molecular breeding studies and developing new high temperature tolerant rice varieties.

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Pre-harvest sprouting (PHS) is one of the important traits that not only cause serious economic issues but also lead to reduction in grain quality and yield in rice (Oryza sativa L.). To analyze the quantitative trait loci (QTLs) for PHS tolerance, we evaluated PHS, seed dormancy (SD), and low-temperature germination (LTG) of 88 F_2:3 populations and their parental lines. Genotypic analysis was performed by using 441 single nucleotide polymorphisms (SNPs) detected from re-sequencing data. Seed dormancy (SD) and low-temperature germination (LTG) were identified to exhibit a positive correlation with PHS. Under the field condition, two major QTLs for PHS, qPHS1-1^FC and qPHS1-2^FC were identified on chromosome 1. Under the growth chamber condition, qPHS1-1^GC and qPHS1-2^GC had the same regions on chromosome 1. QTLs of SD and LTG (qSD1-1, qSD1-2, qLTG1-1, and qLTG1-2) had the same regions; these results suggested that candidate QTLs demonstrate pleiotropy about PHS, SD, and LTG. The major QTLs detected in this study are hypothesized to provide an important resource for molecular breeding and gain a better understanding of the genetics of traits in rice.

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  International Journal of Molecular Sciences.2021; 22(21): 11804.     CrossRef

This study examined the genetic variation of cyanidin 3-glucoside (C3G) contents in blackish-purple rice. F₂ populations were established from crosses between blackish purple rice and normal white rice. The blackish rice cultivars used were Jilinheimi, Heidao38, LK1A-2-12-1-1, Heugjinju, and No2, and the common white rice cultivars used were Hwachung super giant embryo and Heugbal. The purple pericarp color is known to be controlled by a set of dominant alleles, Pb(Prp-b) and Pp(Prp-a). In this study, the segregation of the black purple:brown:white pericarp in the F₂ population was 9:3:4, demonstrating that the purple pericarp color was controlled by two dominant complementary genes. The F₂ distribution of C3G showed continuous variation, with a tendency toward a lower level in all the crosses. However, some F₂ crosses, such as Jilinheimi/Heidao38 and Jilinheimi/LK1A-2-12-1-1, showed transgressive segregation of the C3G content. C3G content of Jilinheimi linked on 84% level in C3G content of F₂ population between Jilinheimi/Heidao38, and 41.3% level in Jilinheimi/LK1A-2-12-1-1. The results of the color difference meter and C3G content analysed by HPLC revealed highly significant correlations between the seed coat color of the colored rice germplasm and that of the segregated populations. There was a significant positive correlation between the C3G content with L* (lightness) and b* (yellowness). The a* (redness) was different in each cross, but there was a significant positive correlation between the C3G content with L* and b*.

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