A High-Density Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population

Harushima, Yoshiaki; Yano, Masahiro; Shomura, Ayahiko; Sato, Mikiko; Shimano, Tomotoshi; Kuboki, Y; Yamamoto, Tetsuro; Lin, Sey‐En; Antonio, Baltazar A.; Parco, Arnold; Kajiya, Hiromi; Huang, Ning; Yamamoto, Kimiko; Nagamura, Yoshiaki; Kurata, Nori; Khush, G. S.; Sasaki, Takuji

doi:10.1093/genetics/148.1.479

Cited by 699 publications

(31 citation statements)

References 54 publications

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“…5 . The linkage map was compared side-to-side with a restriction fragment length polymorphism (RFLP) marker-based high-density linkage map ( Harushima et al 1998 ), in which some markers have been sequenced. Based on the Nipponbare genome sequence (Os-Nipponbare-Reference-IRGSP-1.0) ( Kawahara et al 2013 ), DNA markers located near each other on Nipponbare pseudomolecules are connected with dotted lines.…”

Section: Resultsmentioning

confidence: 99%

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Linkage analysis of rice bacterial blight resistance gene <i>xa20</i> in XM6, a mutant line from IR24

et al. 2021

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Bacterial blight caused by Xanthomonas oryzae pv. oryzae ( Xoo ) is an important disease constraining rice ( Oryza sativa L.) production worldwide. The XM6 line was induced by N-methyl-N-nitrosourea from IR24, an Indica cultivar that is susceptible to Philippine and Japanese Xoo races. XM6 was confirmed to carry a recessive gene named xa20 , resistant to six Philippine and five Japanese Xoo races. The chromosomal gene location was found using 10 plants with the shortest lesion length in an F 2 population consisting of 298 plants from a susceptible Japonica variety Koshihikari × XM6. Analysis using PCR-based DNA markers covering the whole rice genome indicated the gene as located on the distal region of the long arm of chromosome 3. The IKC3 line carries IR24 genetic background with Koshihikari fragment on chromosome 3 where a resistance gene was thought to be located. The F 2 population from IKC3 × XM6 clearly showed a bimodal distribution separating resistant and susceptible plants. Further linkage analysis conducted using this F 2 population revealed that xa20 is located within the 0.8 cM region flanked by DNA markers KIC3-33.88 (33.0 Mb) and KIC3-34.06 (33.2 Mb). This study yields important findings for resistance breeding and for the genetic mechanism of Xoo resistance.

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Section: Resultsmentioning

confidence: 99%

“… Linkage map showing the location of xa20 on chromosome 3. A and B show RFLP framework map of chromosome 3 modified from Harushima et al (1998) ; C represents linkage map of xa20 gene constructed from F 2 population from IKC3 and XM6 ( n = 299). DNA markers located near each other on Nipponbare pseudomolecules are connected by dotted lines.…”

Section: Figmentioning

confidence: 99%

Linkage analysis of rice bacterial blight resistance gene <i>xa20</i> in XM6, a mutant line from IR24

et al. 2021

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“…Several saturated genetic linkage maps based on molecular markers have been developed for rice, using indicaxjapoaica or O. sativaxo. lorzgistantiizata crosses (Causse et al 1994;McCouch et al 1988;Harushima et al 1998). However, no extended linkage study has so far been reported between the two cultivated rice species; only linkage studies on small portions of the genome have been carried using morphological markers (Sano 1990).…”

Section: Introductionmentioning

confidence: 99%

A first interspecific Oryza sativa × Oryza glaberrima microsatellite-based genetic linkage map

Lorieux¹,

Ndjiondjop²,

Ghesquière³

2000

TAG Theoretical and Applied Genetics

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Oryza glaberriina is an endemic African cultivated rice species. To provide a tool for evaluation and utilisation of the potential of O. glaberrinia in rice breeding, we developed an interspecific O. glaberri-inaxOryza sativa genetic linkage map. It was based on PCR markers, essentially microsatellites and STSs. Segregation of markers was examined in a backcross (O. sativalo. glaberrimal10. sativa) population. Several traits were measured on the BC, plants, and major genes and QTLs were mapped for these traits. Several of these genes correspond well to previously identified loci. The overall map length was comparable to those observed in indicaxjaponica crosses, indicating that recombination between the two species occurs without limitation. However, three chromosomes show discrepancies with the iizdicaxjaponica maps. The colinearity with intraspecific maps was very good, confirming previous cytological observations. A strong segregation-distortion hot spot was observed on chromosome 6 near the waxy gene, indicating the presence of sl o. a sporo-gametophytic sterility gene previously identified by Sano (1990). The main interests of such a PCR-based map for African rice breeding are discussed, including gene and QTL localisation, marker-assisted selection, and the development of interspecific introgression lines. Key words O. glaberrirna . O. sativa. Rice . Genetic maps . Microsatellites . Sequence-tagged sites . Interspecific hybridisation . GenelQTL mapping+ Segregation distortion Communicated by H.F. Linskens M. Lorieux (€33) . M.-N. Ndjiondjop . A.

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“…A fosmid library constructed from BIL680 was screened with two DNA markers, C213 and C728 (Table S2; Harushima et al., 1998). Consequently, four clones (Fos1, 2, 10 and 12) were identified.…”

Section: Resultsmentioning

confidence: 99%

Vigorous growth and high yielding of rice (Oryza sativa) introgression lines and transformants carrying a PRR37 allele from wild rice O. longistaminata

et al. 2021

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Wild rice species are expected to possess genes that are potentially useful for rice breeding. Backcross inbred lines (BILs) derived from a cross of a japonica rice ‘Shiokari’ and a progeny line from a cross of a japonica ‘Taichung 65’ and Oryza longistaminata MwM were examined for agronomic traits. Some BILs showed vigorous growth and increased yield relative to ‘Shiokari’. One of such BILs was further analysed using QTL mapping followed by map‐based cloning to identify the causal gene. An allele of OsPRR37, which encodes a pseudo response regulator protein, in O. longistaminata was found responsible for the traits and named OlPRR37. OlPRR37 was expressed more than an OsPRR37 allele from a japonica ‘Nipponbare’ in the heterozygotes of the two alleles. The genomic clone of OlPRR37 and the coding sequences of both OlPRR37 and the ‘Nipponbare’ allele driven by the promoter of OlPRR37 similarly functioned as high‐yielding genes in transgenic rice. Thus, higher expression of PRR37 by the OlPRR37 promoter likely conferred the increased yield. Accordingly, OlPRR37 may be used to improve rice productivity.

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A High-Density Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population

Cited by 699 publications

References 54 publications

Linkage analysis of rice bacterial blight resistance gene <i>xa20</i> in XM6, a mutant line from IR24

Linkage analysis of rice bacterial blight resistance gene <i>xa20</i> in XM6, a mutant line from IR24

A first interspecific Oryza sativa × Oryza glaberrima microsatellite-based genetic linkage map

Vigorous growth and high yielding of rice (Oryza sativa) introgression lines and transformants carrying a PRR37 allele from wild rice O. longistaminata

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