Detection of Quantitative Trait Loci for White-back and Basal-white Kernels under High Temperature Stress in japonica Rice Varieties

Kobayashi, Asako; Bao, Guolian; Ye, Shenghai; Tomita, Katsura

doi:10.1270/jsbbs.57.107

Cited by 71 publications

(54 citation statements)

References 12 publications

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“…No polymorphic marker on the short arm of chromosome 9 was detected. Kobayashi et al (2007) and Tabata et al (2007) reported similar results for chromosome 9 in temperate japonica crosses, suggesting that chromosome 9 may be highly monomorphic and common by descent in japonica rice.…”

Section: Discussionmentioning

confidence: 64%

QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.)

et al. 2008

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To employ molecular marker-aided selection for developing japonica rice (Oryza sativa L.) cultivars with high yielding potential and good eating quality, we carried out QTL analysis for agronomic and grain traits using 231 recombinant inbred lines (RIL) from a cross between two temperate japonica cultivars, Suweon365 and Chucheongbyeo. A linkage map with 221 loci, including 134 simple sequence repeats (SSRs), 66 amplified fragment length polymorphisms (AFLPs), and 21 miniature inverted repeat transposable elements (MITEs)-anchored markers, was constructed covering 2,227 cM of the twelve rice chromosomes, with an average distance of 11.0 cM between markers. The proportion of polymorphic bands between parents averaged 19.5%, 12.9% and 42.3% for SSRs, AFLPs and MITEs, respectively. Construction of maps without AFLP or MITE markers indicated that expansion of this map is due to the incorporation of AFLP markers, and this result is consistent with previous reports. Twenty-seven QTLs for ten traits were identified over two years, and fourteen were consistently detected in two consecutive years. When the locations of each QTL detected in this study were compared with those in previous QTLs studies, eight QTLs for culm length, spikelets per panicle and, thickness, length and shape of grain, had not been reported in previous mapping studies, indicating potentially novel alleles of japonica rice. Interestingly, a cluster of seven QTLs, including heading date and grain morphology traits, was detected on the long arm of chromosome 7. The markers linked to these QTLs would be valuable in a marker-assisted breeding program for japonica cultivars.

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Section: Discussionmentioning

confidence: 64%

QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.)

et al. 2008

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“…Recently, biparental populations of Japanese rice cultivars have been used for genetic analysis of the natural variation in several agronomic traits, such as heading date (Fujino et al 2005, Matsubara et al 2008, culm length (Hori et al 2009), pre-harvest sprouting resistance (Hori et al 2010), eating quality (Kobayashi and Tomita 2008, Takeuchi et al 2008, Wada et al 2008) and grain quality (Kobayashi et al 2007, Tabata et al 2007). These studies have demonstrated that a relatively large allelic difference at a particular locus could be detected despite extremely low sequence diversity in Japanese cultivars.…”

Section: Discussionmentioning

confidence: 99%

Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population

et al. 2010

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To analyze genetic features in the Japanese rice population, which is mainly composed of closely related accessions, a core set of single-nucleotide polymorphisms (SNPs) was selected from SNP resources based on Japanese rice cultivars. A total of 25,199 SNPs were newly detected from the comparison of genomic sequences between two cultivars (Eiko and Rikuu132) and Nipponbare as a reference. A total of 81,499 nonredundant SNPs, including 67,051 SNPs of Koshihikari detected in a previous study, were used as candidates to select the core SNPs. Across the entire genome, 3379 SNPs were selected based on the chromosomal position of each SNP and were investigated each allele of 92 Japanese rice accessions and 3 from outside of Japan. As a result, 2551 SNPs were found to be informative for at least 91 cultivars for reducing the potential risks of genotyping error. The Japanese rice accessions were classified into three groups (upland, lowland Hokkaido, and other lowland) using all 2551 SNPs. In addition, a core set of 768 SNPs was selected to provide an even distribution among the chromosomes. Comparison of dendrograms generated by all 2551 SNPs and the core set of 768 SNPs demonstrated that the core SNPs could be used efficiently and reliably in the classification of the Japanese rice population. The core SNPs can be used for diversity analysis and for genetic analysis of the biparental populations of Japanese rice accessions.

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“…For simple sequence repeat (SSR) analysis to construct a linkage map, PCR was performed as described in Kobayashi et al (2007).…”

Section: Marker and Statistical Analysesmentioning

confidence: 99%

QTL detection for stickiness of cooked rice using recombinant inbred lines derived from crosses between japonica rice cultivars

Kobayashi¹,

Tomita²

2008

Breed. Sci.

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To establish a marker-assisted selection system for the eating quality of cooked rice, we performed quantitative trait locus (QTL) analysis using 188 recombinant inbred lines (RILs) derived from crosses of two japonica cultivars, 'Sakihikari' and 'Nipponbare'. The former has excellent eating quality with strong stickiness whereas the latter is less sticky. We evaluated the stickiness of cooked rice using a sensory test, as well as amylose content (AC), amylographic characteristics (AM), and days-to-heading of RILs, which affect stickiness, in 2005, 2006 and 2007, and used them for QTL analysis. Six QTLs for stickiness were identified on chromosomes 1, 3 (two QTLs), 6, 7 and 8. Of these, qST3-1 on the short arm of chromosome 3 was detected throughout the three-year experiments but the others were detected in one year only. We also mapped two QTLs for AC, 19 QTLs for AM, and three QTLs for days-to-heading. Stickiness of RILs was significantly correlated with AM, and several QTLs for AM were detected in the same QTL regions for stickiness. These results thus suggested that AM was important for the stickiness of RILs. The obtained QTL information is useful to identify DNA markers tightly linked to genes controlling eating quality.

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Detection of Quantitative Trait Loci for White-back and Basal-white Kernels under High Temperature Stress in japonica Rice Varieties

Cited by 71 publications

References 12 publications

QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.)

QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.)

Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population

QTL detection for stickiness of cooked rice using recombinant inbred lines derived from crosses between japonica rice cultivars

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