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Grain shape is one of the key factors deciding the yield product and the market value as appearance quality in rice (Oryza sativa L.). The grain shape of japonica cultivars in Korea is quite monotonous because the selection pressure of rice breeding programs works in consideration of consumer preference. In this study, we identified QTLs associated with grain shape to improve the variety of grain shapes in Korean cultivars. QTL analysis revealed that eight QTLs related to five tested traits were detected on chromosomes 2, 5, and 10. Among them, three QTLs—qGL2 (33.9% of PEV for grain length), qGW5 (64.42% for grain width), and qGT10 (49.2% for grain thickness)—were regarded as the main effect QTLs. Using the three QTLs, an ideal QTL combination (qGL2P + qGW5P + qGT10B) could be constructed on the basis of the accumulated QTL effect without yield loss caused by the change in grain shape in the population. In addition, three promising lines with a slender grain type were selected as a breeding resource with a japonica genetic background based on the QTL combination. The application of QTLs detected in this study could improve the grain shape of japonica cultivars without any linkage drag or yield loss. [ABSTRACT FROM AUTHOR]

For the purpose of breeding documentation, researchers and breeders kept handwritten records of the breeding history, including parental information and breeding methods. The cultivars were used again as parents for further breeding, and modern cultivars of rice have a wide range of alleles from many generations of parents and ancestors. To understand such a breeding history, it is necessary to ask around for relevant information, which is then usually documented in Excel or Word by multiple breeders or breeding institutes. Here, we constructed RicePedigree, which contains the breeding history of rice based on the documents provided by the Rural Development Administration (RDA) in Korea. We devised a simple method for collecting a breeding history and storing it in a database. RicePedigree is a web-based application on the database that facilitates researchers' and breeders' utilization of the breeding history of rice. Based on the query cultivar name, it will return a hierarchical tree of breeding histories and a list of cultivars and breeding lines that contain query cultivars in their breeding histories. This app would be a good way to review and keep track of information about current and future cultivars. [ABSTRACT FROM AUTHOR]

‘Haedeul’ is a high-quality rice variety with early maturing that adapts to the central region of Korea. This cultivar was crossed between ‘Gopum’, which has excellent taste, and ‘Hoban’, which has a low viviparous germination rate and is moderately tolerant of cold, by the rice breeding team of the Department of Central Area Crop Science, NlCS, RDA, in 2017. In early-transplanting cultivation, the heading date of ‘Haedeul’ was July 24 in central area of Korea, which was seven days later than that of ‘Jopyeong’. ‘Haedeul’ had a culm length of 75 cm and 99 spikelets per panicle. The viviparous germination rate of ‘Haedeul’ was 7.7%. It showed resistance to blast and bacterial blight (K1, K2, K3 race), but was susceptible to the K3a race of bacterial blight, stripe virus, dwarf and black streak dwarf viruses, and plant-hoppers. The milled rice of this variety exhibited a translucent and medium short grain shape. The cooked rice grains of ‘Haedeul’ had an excellent palatability index (0.61) and lower amylose content (18.0%) than that of ‘Jopyeong’. The grain milling characteristics were better than those of ‘Jopyeong’, especially the head rice milling recovery ratio and head rice ratio (94.9%). ‘Haedeul’ milled rice productivity averaged 5.32 MT/ha at five sites under ordinary cultivation. [ABSTRACT FROM AUTHOR]

Rice blast is one of the most serious agricultural diseases in the world. Rice blast can be managed using low nitrogen fertilizers, treatment with chemical fungicides, and the most effective resistant varieties. Many genetic resources have been investigated and used along with molecular markers to breed blast-resistant rice varieties. In this study, the genetic diversity of blast resistance genes using 27 functional/linked markers and rice blast incidence over three years was investigated in 296 Korean rice varieties. Blast incidence was determined using a 0-9 scoring system (0=no lesions to 9=dead leaves) in nursery tests. The blast incidence of 296 rice varieties showed a significant correlation between years (r>0.64, p<0.001). The 261 Japonica varieties showed blast resistance compared to 114 mid-late maturing varieties or 96 medium-maturing varieties. 35 Tongil-type varieties also exhibited greater resistance than Japonica varieties. DNA marker-trait association analysis was conducted using 27 DNA markers linked to 19 blast resistance genes. Twelve DNA markers showed significant associations with the average blast incidence over 3 years. The ‘9871.T7E’ marker linked with Pi40 was strongly associated with blast disease, with a phenotypic variance of 24% over 3 years (p<0.001). Among the varieties harboring the Pi40 allele, early maturing varieties accounted for 87%. These results imply that the blast resistance of early maturing Korean varieties is associated with the Pi40 gene. These results will be beneficial for breeding blast-resistant rice in Korea. [ABSTRACT FROM AUTHOR]

Temperate japonica is used as the parent for crossing in the breeding of new rice cultivars in Korea, and the grain shape of the developed lines or cultivars is a semi-round and medium-short grain length. To overcome the current low quantity of japonica cultivar germplasm and deterioration in quality caused by climate change, it is necessary to diversify the grain characteristics of japonica. Most of the United States (US) cultivars are classified as medium, long, extra-long, and half spindle- and spindle-shaped grains. The qSW5 allelotype, a major gene involved in grain width, is found in all US cultivars. In addition, the US cultivar ‘Saber’ has both qgl3 and GS3_B alleles, which have low allele frequencies among Korean rice cultivars, and ‘A020’ had gw8, an allele with a reduced grain width. The pasting properties and texture of medium-grain length and half-spindle-shaped cultivars were relatively similar to those of the Korean rice cultivar, but different from those of long-grain and long spindle-shaped cultivars. Therefore, grain shape is associated with pasting properties and texture traits. Among the rice cultivars in the US, tropical japonica belongs to the same japonica as the Korean rice cultivar; however, its grain shape is similar to that of indica. As grain shape is also related to grain quality, US cultivars can be used as a useful genetic resource for diversifying the grain characteristics of Korean japonica cultivars and breeding new cultivars. [ABSTRACT FROM AUTHOR]

Revealing genomic variation of representative and diverse germplasm is the cornerstone of deploying genomics information into genetic improvement programs of species of agricultural importance. Here we report the re-sequencing of 239 japonica rice elites representing the genetic diversity of japonica germplasm in China, Japan and Korea. A total of 4.8 million SNPs and PAV of 35,634 genes were identified. The elites from Japan and Korea are closely related and relatively less diverse than those from China. A japonica rice pan-genome was constructed, and 35 Mb non-redundant novel sequences were identified, from which 1131 novel genes were predicted. Strong selection signals of genomic regions were detected on most of the chromosomes. The heading date genes Hd1 and Hd3a have been artificially selected during the breeding process. The results from this study lay the foundation for future whole genome sequences-enabled breeding in rice and provide a paradigm for other species. • A set of 239 diverse japonica rice elites was re-sequenced, and 4.8 million SNPs and PAV of 35,634 genes were identified. • The elites from Japan and Korea are closely related and relatively less diverse than those from Northeast China. • A japonica rice pan-genome was constructed, and 1131 full-length novel genes were predicted from 35 Mb non-redundant novel sequences. • Strong selection signals of genomic regions were detected on most of the chromosomes. [ABSTRACT FROM AUTHOR]

Rice is the most important staple food in Korea. Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases in the rice-growing world and in Korea. Eighteen major blast resistance genes were screened in 33 leading Korean japonica varieties using 44 DNA markers. The 33 leading japonica varieties are cultivated in 659,642 ha (90.4%), and a variety of Samkwang is cultivated widely on a nation-wide scale. Four resistance genes, Pia, Pib, Pi19, and Pb1, were detected in 10-21 varieties, and the R-genes of Pii, Pish, Pita/Pita-2, Piz/Piz-t, Pi35, and Pi65(t), were present in 2-5 varieties. Five R-genes, Pit, Pi5, Pi9, pi21, and Pi40, were not detected in the Korean japonica rice varieties. A total of six varieties, two mid-late flowering varieties, Ilmi and Saeilmi, a medium flowering variety Gopum; and three early flowering varieties Jopyeong, Haedamssal, and Haedeul; were resistant to blast nursery screening over 12 years. A variety of Gopum harbored alleles for Piz/Piz-t, and three early flowering varieties, Jopyeong, Haedamssal, and Haedeul, had extensive loci of the multiple-gene family Piz/Piz-t, Pi9, and Pi40 on chromosome 6. Two mid-late flowering varieties, Ilmi and Saeilmi, harbored the Pita-2 gene, and Gopum had Pita. In the japonica rice breeding program, an effective means for enhancing stable resistance to blast would be introduced to 2-3 R genes among resistance genes Pit, Pi5, Pi9, pi21 and Pi40 which were not identified in Korean japonica rice varieties, and resistance genes Pita/Pita-2, Piz-t/Piz-5, to 2-3 R genes among and Pi20 that showed stable resistance in monogenic IRBL lines. [ABSTRACT FROM AUTHOR]