Heterogeneous inbred family (HIF) analysis: a method for developing near-isogenic lines that differ at quantitative trait loci

Tuinstra, Mitchell R.; Ejeta, Gebisa; Goldsbrough, Peter B.

doi:10.1007/s001220050654

Cited by 304 publications

(264 citation statements)

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“…Together with the identification of a recombination between cfb341 and the GBR0233 marker within a single BAC in the SSD population, these results also suggest high recombination rates in the SKr region, which should greatly support efficient map-based cloning of the gene. We are developing currently a heterogeneous inbred family population (Tuinstra et al 1997) using a line (SSD254) heterozygous for the molecular markers GBR0233, cfb341, cfb306, gwm234, E41M48, dl103, fbb267, and bcd873 that flank SKr (W. Alfares and C. Feuillet, unpublished data) and carrying the alleles from Courtot for the other loci on 5BS.…”

Section: Resultsmentioning

confidence: 99%

Fine Mapping and Marker Development for the Crossability Gene SKr on Chromosome 5BS of Hexaploid Wheat (Triticum aestivum L.)

et al. 2009

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Most elite wheat varieties cannot be crossed with related species thereby restricting greatly the germplasm that can be used for alien introgression in breeding programs. Inhibition to crossability is controlled genetically and a number of QTL have been identified to date, including the major gene Kr1 on 5BL and SKr, a strong QTL affecting crossability between wheat and rye on chromosome 5BS. In this study, we used a recombinant SSD population originating from a cross between the poorly crossable cultivar Courtot (Ct) and the crossable line MP98 to characterize the major dominant effect of SKr and map the gene at the distal end of the chromosome near the 5B homeologous GSP locus. Colinearity with barley and rice was used to saturate the SKr region with new markers and establish orthologous relationships with a 54-kb region on rice chromosome 12. In total, five markers were mapped within a genetic interval of 0.3 cM and 400 kb of BAC contigs were established on both sides of the gene to lay the foundation for map-based cloning of SKr. Two SSR markers completely linked to SKr were used to evaluate a collection of crossable wheat progenies originating from primary triticale breeding programs. The results confirm the major effect of SKr on crossability and the usefulness of the two markers for the efficient introgression of crossability in elite wheat varieties.

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Section: Resultsmentioning

confidence: 99%

Fine Mapping and Marker Development for the Crossability Gene SKr on Chromosome 5BS of Hexaploid Wheat (Triticum aestivum L.)

et al. 2009

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“…To validate the obtained loci, we developed heterogeneous inbred families (HIFs; Tuinstra et al, 1997) from RILs with residual heterozygosity within QTL intervals (for all HIFs, see Supplemental Table S6; for primers used, see Supplemental Table S7). Three low-K-specific MR loci were validated with HIFs 49, 178, and 479 and one low-K-specific LR locus was validated with HIF 434 (Fig.…”

Section: Strategies I and Ii Are Characterized By Cell Death Around Tmentioning

confidence: 99%

“…RILs with residual heterozygosity in QTL intervals were selected to produce HIFs (Tuinstra et al, 1997). All RILs were grown on soil, and seeds from individuals harboring the homozygous Col-0 or Ct-1 allele at the corresponding locus were harvested and phenotyped on control and low-K plates.…”

Section: Generation Of Hifsmentioning

confidence: 99%

Natural Variation of Arabidopsis Root Architecture Reveals Complementing Adaptive Strategies to Potassium Starvation

2013

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Root architecture is a highly plastic and environmentally responsive trait that enables plants to counteract nutrient scarcities with different foraging strategies. In potassium (K) deficiency (low K), seedlings of the Arabidopsis (Arabidopsis thaliana) reference accession Columbia (Col-0) show a strong reduction of lateral root elongation. To date, it is not clear whether this is a direct consequence of the lack of K as an osmoticum or a triggered response to maintain the growth of other organs under limiting conditions. In this study, we made use of natural variation within Arabidopsis to look for novel root architectural responses to low K. A comprehensive set of 14 differentially responding root parameters were quantified in K-starved and Kreplete plants. We identified a phenotypic gradient that links two extreme strategies of morphological adaptation to low K arising from a major tradeoff between main root (MR) and lateral root elongation. Accessions adopting strategy I (e.g. Col-0) maintained MR growth but compromised lateral root elongation, whereas strategy II genotypes (e.g. Catania-1) arrested MR elongation in favor of lateral branching. K resupply and histochemical staining resolved the temporal and spatial patterns of these responses. Quantitative trait locus analysis of K-dependent root architectures within a Col-0 3 Catania-1 recombinant inbred line population identified several loci each of which determined a particular subset of root architectural parameters. Our results indicate the existence of genomic hubs in the coordinated control of root growth in stress conditions and provide resources to facilitate the identification of the underlying genes.

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“…The use of NILs that differ at a single QTL is an effective approach for fine mapping and characterization of an individual locus (Salvi and Tuberosa 2005). However, the development of NILs through repeated backcrossing is time-consuming and laborious (Tuinstra et al 1997). The use of a residual heterozygous line (RHL), as proposed by Yamanaka et al (2004), and which is derived from RIL, is a powerful tool for precisely evaluating QTL (Haley et al 1994).…”

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confidence: 99%

Map-Based Cloning of the Gene Associated With the Soybean Maturity Locus E3

et al. 2009

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Photosensitivity plays an essential role in the response of plants to their changing environments throughout their life cycle. In soybean [Glycine max (L.) Merrill], several associations between photosensitivity and maturity loci are known, but only limited information at the molecular level is available. The FT3 locus is one of the quantitative trait loci (QTL) for flowering time that corresponds to the maturity locus E3. To identify the gene responsible for this QTL, a map-based cloning strategy was undertaken. One phytochrome A gene (GmPhyA3) was considered a strong candidate for the FT3 locus. Allelism tests and gene sequence comparisons showed that alleles of Misuzudaizu (FT3/FT3; JP28856) and Harosoy (E3/E3; PI548573) were identical. The GmPhyA3 alleles of Moshidou Gong 503 (ft3/ft3; JP27603) and L62-667 (e3/e3; PI547716) showed weak or complete loss of function, respectively. High red/far-red (R/FR) long-day conditions enhanced the effects of the E3/FT3 alleles in various genetic backgrounds. Moreover, a mutant line harboring the nonfunctional GmPhyA3 flowered earlier than the original Bay (E3/E3; PI553043) under similar conditions. These results suggest that the variation in phytochrome A may contribute to the complex systems of soybean flowering response and geographic adaptation.

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Heterogeneous inbred family (HIF) analysis: a method for developing near-isogenic lines that differ at quantitative trait loci

Cited by 304 publications

References 10 publications

Fine Mapping and Marker Development for the Crossability Gene SKr on Chromosome 5BS of Hexaploid Wheat (Triticum aestivum L.)

Fine Mapping and Marker Development for the Crossability Gene SKr on Chromosome 5BS of Hexaploid Wheat (Triticum aestivum L.)

Natural Variation of Arabidopsis Root Architecture Reveals Complementing Adaptive Strategies to Potassium Starvation

Map-Based Cloning of the Gene Associated With the Soybean Maturity Locus E3

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