Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice

Brès, Cécile; Lorieux, Mathias; Clément, Guy; Bangratz, Martine; Ghesquière, Alain

doi:10.1007/s001220051626

Cited by 98 publications

(83 citation statements)

References 31 publications

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“…A comparative QTL analysis of rice heading-date QTL on the short arm of chromosome 1 reveals several other published QTL in the same region as dth1.1. Of 17 rice QTL studies examined Xiao et al 1995Xiao et al , 1996Xiao et al , 1998Kohn et al 1997;Lu et al 1997;Yano et al 1997;Doi et al 1998;Lin et al 1998;Xiong et al 1999;Maheswaran et al 2000;Bres-Patry et al 2001;Moncada et al 2001;Cai and Morishima 2002;Yu et al 2002;Hittalmani et al 2003;Septiningsih et al 2003), five heading-date QTL were identified in the dth1.1 region, four of which were detected in interspecific crosses in rice (Kohn et al 1997;Doi et al 1998;Xiao et al 1998;Cai and Morishima 2002) and one in an intraspecific cross (Maheswaran et al 2000). Interestingly, in the thoroughly studied intraspecific Nipponbare/Kasalath population, 14 heading-date QTL have been identified, none of which are located on chromosome 1 (Yano 2001).…”

Section: Discussionmentioning

confidence: 99%

Substitution Mapping of dth1.1, a Flowering-Time Quantitative Trait Locus (QTL) Associated With Transgressive Variation in Rice, Reveals Multiple Sub-QTL

Thomson

Edwards²,

Septiningsih³

et al. 2006

Genetics

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A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short-and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT, SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait.

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Section: Discussionmentioning

confidence: 99%

Substitution Mapping of dth1.1, a Flowering-Time Quantitative Trait Locus (QTL) Associated With Transgressive Variation in Rice, Reveals Multiple Sub-QTL

Thomson

Edwards²,

Septiningsih³

et al. 2006

Genetics

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“…SSRs are highly polymorphic genetic markers and because of their widespread distribution in the genome, high allelic diversity and inherent potential have become a valuable source of genetic markers. SSR markers have been applied to analyze diversity (Cho et al, 2000;Harrington, 2000) and to locate genes and quantitative trait loci (QTLs) on rice chromosomes (Zou et al, 2000;Bres-Patry et al, 2001;Moncada et al, 2001). Several microsatellite markers with publicly available databases closely linked with the Pi-b, Pi-k h and Pi-ta 2 resistance genes have been identified (Fjellstrom et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Analysis of simple sequence repeat markers linked with blast disease resistance genes in a segregating population of rice (Oryza sativa)

Ashkani¹,

Rafii²,

Meon³

et al. 2011

Genet. Mol. Res.

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ABSTRACT. Among 120 simple sequence repeat (SSR) markers, 23 polymorphic markers were used to identify the segregation ratio in 320 individuals of an F 2 rice population derived from Pongsu Seribu 2, a resistant variety, and Mahsuri, a susceptible rice cultivar. For phenotypic study, the most virulent blast (Magnaporthe oryzae) pathotype, P7.2, was used in screening of F 2 population in order to understand the inheritance of blast resistance as well as linkage with SSR markers. Only 11 markers showed a good fit to the expected segregation ratio (1:2:1) for the single gene model (d.f. = 1.0, P < 0.05) in chi-square (χ 2 ) analyses. In the phenotypic data analysis, the F 2 population segregated in a 3:1 (R:S) ratio for resistant and susceptible plants, respectively. Therefore, resistance to blast pathotype P7.2 in Pongsu Seribu 2 is most likely controlled by a single nuclear gene. The plants from F 2 lines that showed resistance to blast pathotype P7.2 were linked to six alleles of SSR markers, RM168 (116 bp), RM8225 (221 bp), RM1233 (175 bp), RM6836 (240 bp), RM5961 (129 bp), and RM413 (79 bp). These diagnostic markers could be used in marker assisted selection programs to develop a durable blast resistant variety.

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“…Previous studies in rice have contributed to the development of several hundred microsatellite markers and a genetic map consisting of 320 SSRs (Wu and Tanksley 1993;Akagi et al 1996;Panaud et al 1996;Chen et al 1997;Temnykh et al 2000). These markers have been used to analyze diversity (Yang et al 1994;Olufowote et al 1997;Cho et al 2000;Harrington 2000) and to locate genes and QTLs on rice chromosomes using both intra-and interspecific crosses (Xiao et al 1998;Bao et al 2000;Zou et al 2000;Bres-Patry et al 2001;Moncada et al 2001). SSRs are increasingly useful for integrating the genetic, physical, and sequence-based maps of rice, and they simultaneously provide breeders and geneticists with an efficient tool to link phenotypic and genotypic variation.…”

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confidence: 99%

Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential

Temnykh¹,

DeClerck²,

Lukashova³

et al. 2001

Genome Res.

1,351

1,028

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A total of 57.8 Mb of publicly available rice (Oryza sativa L.) DNA sequence was searched to determine the frequency and distribution of different simple sequence repeats (SSRs) in the genome. SSR loci were categorized into two groups based on the length of the repeat motif. Class I, or hypervariable markers, consisted of SSRs Ն20 bp, and Class II, or potentially variable markers, consisted of SSRs Ն12 bp <20 bp. The occurrence of Class I SSRs in end-sequences of EcoRI-and HindIII-digested BAC clones was one SSR per 40 Kb, whereas in continuous genomic sequence (represented by 27 fully sequenced BAC and PAC clones), the frequency was one SSR every 16 kb. Class II SSRs were estimated to occur every 3.7 kb in BAC ends and every 1.9 kb in fully sequenced BAC and PAC clones. GC-rich trinucleotide repeats (TNRs) were most abundant in protein-coding portions of ESTs and in fully sequenced BACs and PACs, whereas AT-rich TNRs showed no such preference, and di-and tetranucleotide repeats were most frequently found in noncoding, intergenic regions of the rice genome. Microsatellites with poly(AT)n repeats represented the most abundant and polymorphic class of SSRs but were frequently associated with the Micropon family of miniature inverted-repeat transposable elements (MITEs) and were difficult to amplify. A set of 200 Class I SSR markers was developed and integrated into the existing microsatellite map of rice, providing immediate links between the genetic, physical, and sequence-based maps. This contribution brings the number of microsatellite markers that have been rigorously evaluated for amplification, map position, and allelic diversity in Oryza spp. to a total of 500.[Clone sequences for 199 markers (RM1-RM88, RM200-RM345) developed in this lab are available as GenBank accessions AF343840-AF343869 and AF344003-AF344169.]Microsatellites are tandemly arranged repeats of short DNA motifs (1-6 bp in length) that frequently exhibit variation in the number of repeats at a locus. Because of their abundance and inherent potential for variation, these simple sequence repeats (SSRs) have become a valuable source of genetic markers. Previous studies in rice have contributed to the development of several hundred microsatellite markers and a genetic map consisting of 320

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Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice

Cited by 98 publications

References 31 publications

Substitution Mapping of dth1.1, a Flowering-Time Quantitative Trait Locus (QTL) Associated With Transgressive Variation in Rice, Reveals Multiple Sub-QTL

Substitution Mapping of dth1.1, a Flowering-Time Quantitative Trait Locus (QTL) Associated With Transgressive Variation in Rice, Reveals Multiple Sub-QTL

Analysis of simple sequence repeat markers linked with blast disease resistance genes in a segregating population of rice (Oryza sativa)

Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential

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