Identification of a large cluster of coiled coil-nucleotide binding site–leucine rich repeat-type genes from the Rps1 region containing Phytophthora resistance genes in soybean

Bhattacharyya, Madan K.; Narayanan, Narayanan N.; Gao, Hongyu; Santra, Dipak K.; Salimath, S. S.; Kasuga, Takao; Liu, Y.; Espinosa, Bonnie G.; Ellison, Lori; Marek, Laura F.; Shoemaker, Randy C.; Gijzen, Mark; Buzzell, R. I.

doi:10.1007/s00122-005-1993-9

Cited by 60 publications

(45 citation statements)

References 47 publications

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“…These data suggested that reduced levels of anthocyanin pigments in w4 mutants ( Figure 2A) were the results of lower DFR2 expression levels. Characterization of T322 (w4-m) and its revertants suggested that DFR2 is located in the W4 locus: DFR2 was isolated from a BAC library (Bhattacharyya et al 2005). BAC GS_60E6 was selected for sequencing the entire DFR2 gene (EF187612), which contains six exons and five introns ( Figure 3A).…”

Section: Resultsmentioning

confidence: 99%

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Excision of an Active CACTA-Like Transposable Element From DFR2 Causes Variegated Flowers in Soybean [Glycine max (L.) Merr.]

Brar

Grosic

et al. 2010

Genetics

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Active endogenous transposable elements, useful tools for gene isolation, have not been reported from any legume species. An active transposable element was suggested to reside in the W4 locus that governs flower color in soybean. Through biochemical and molecular analyses of several revertants of the w4-m allele, we have shown that the W4 locus encodes dihydroflavonol-4-reductase 2 (DFR2). w4-m has arisen through insertion of Tgm9, a 20,548-bp CACTA-like transposable element, into the second intron of DFR2. Tgm9 showed high nucleic acid sequence identity to Tgmt *. Its 59 and 39 terminal inverted repeats start with conserved CACTA sequence. The 39 subterminal region is highly repetitive. Tgm9 carries TNP1-and TNP2-like transposase genes that are expressed in the mutable line, T322 (w4-m). The element excises at a high frequency from both somatic and germinal tissues. Following excision, reinsertions of Tgm9 into the DFR2 promoter generated novel stable alleles, w4-dp (dilute purple flowers) and w4-p (pale flowers). We hypothesize that the element is fractured during transposition, and truncated versions of the element in new insertion sites cause stable mutations. The highly active endogenous transposon, Tgm9, should facilitate genomics studies specifically that relate to legume biology. Figure 1) and purple hypocotyls. Mutations at the W4 locus in the W1_ background result in altered pigment accumulation patterns in petals and reduced levels of purple pigments in flowers and hypocotyls. Four mutant alleles, w4, w4-m, w4-dp, and w4-p have been mapped to this locus. The w4 allele represents a spontaneous mutation, which produces near-white flowers (Figure 1) and green hypocotyls (Hartwig and Hinson 1962;Groose and Palmer 1991). The w4-m allele was identified from a cross between two experimental breeding lines with white and purple flowers, respectively (Palmer et al. 1989;Weigelt et al. 1990). w4-m is characterized by variegated flowers (Figure 1) and green hypocotyls with purple sectors (Groose et al. 1988).w4-m has been proposed to harbor a class II transposable element (Palmer et al. 1989). Presumably, somatic excision of the putative transposable element results in the variegated (Groose et al. 1988) and germinal excision wild-type phenotypes, purple flowers and purple pigments on hypocotyls (Palmer et al. 1989;Groose et al. 1990). The mutable line carrying w4-m undergoes germinal reversion at a very high frequency, about 6% per generation ). Approximately 1% of the progeny derived from germinal revertants contain new mutations in unlinked loci, presumably resulting from reinsertion of the element (Palmer et al. 1989). For example, female partial-sterile 1 (Fsp1), female partial-sterile 2 (Fsp2), female partialsterile 3 (Fsp3), and female partial-sterile 4 (Fsp4) were isolated from progenies of germinal revertants with purple flowers and were mapped to molecular linkage groups (MLG) C2, A2, F, and G, respectively (Kato and Palmer 2004). Similarly, 36 male-sterile, female-sterile mutants mapped to t...

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Section: Resultsmentioning

confidence: 99%

“…BAC library screening and W4 gene cloning: A BAC library (Bhattacharyya et al 2005) was screened using a partial DFR cDNA probe (Table S2). Positive clones were confirmed by DNA blot analysis.…”

Section: Methodsmentioning

confidence: 99%

Excision of an Active CACTA-Like Transposable Element From DFR2 Causes Variegated Flowers in Soybean [Glycine max (L.) Merr.]

Brar

Grosic

et al. 2010

Genetics

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“…Unequal crossing-over points were found to locate primarily within intergenic regions [83,84]. Unequal crossoverdriven gene evolution has been reported in a number of other disease resistance gene families across different plant species, including the gene families at the Arabidopsis locus RPP5 [85], the soybean (Glycine max) loci Rps [86,87] and Rsv1 [88], the lettuce (Lactuca sativa) Dm3 locus [89,90], the barley (Hordeum vulgare) Hv-elF4E locus [91], and the citrus Ctv locus [69]. Similarly, unequal crossing-over takes place in gene families other than disease resistance gene families and generates novel haplotypes and alleles at those loci [70,74,75,92].…”

Section: Unequal Crossing-overmentioning

confidence: 94%

Meiosis-Driven Genome Variation in Plants

Cai¹,

Xu²

2007

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Meiosis includes two successive divisions of the nucleus with one round of DNA replication and leads to the formation of gametes with half of the chromosomes of the mother cell during sexual reproduction. It provides a cytological basis for gametogenesis and inheritance in eukaryotes. Meiotic cell division is a complex and dynamic process that involves a number of molecular and cellular events, such as DNA and chromosome replication, chromosome pairing, synapsis and recombination, chromosome segregation, and cytokinesis. Meiosis maintains genome stability and integrity over sexual life cycles. On the other hand, meiosis generates genome variations in several ways. Variant meiotic recombination resulting from specific genome structures induces deletions, duplications, and other rearrangements within the genic and non-genic genomic regions and has been considered a major driving force for gene and genome evolution in nature. Meiotic abnormalities in chromosome segregation lead to chromosomally imbalanced gametes and aneuploidy. Meiotic restitution due to failure of the first or second meiotic division gives rise to unreduced gametes, which triggers polyploidization and genome expansion. This paper reviews research regarding meiosis-driven genome variation, including deletion and duplication of genomic regions, aneuploidy, and polyploidization, and discusses the effect of related meiotic events on genome variation and evolution in plants. Knowledge of various meiosis-driven genome variations provides insight into genome evolution and genetic variability in plants and facilitates plant genome research.

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“…orthologous relationships between these gene family members, even within intraspecific comparisons. The variation in gene content has often necessitated the construction of bacterial artificial chromosome libraries specific to the resistant accession in order to clone specific R genes (Ashfield et al, 2003(Ashfield et al, , 2004Bhattacharyya et al, 2005), even from species with a sequenced reference genome (Ashikawa et al, 2008;Lee et al, 2009). A number of previous studies on specific resistance loci have shown that the genes conferring disease resistance are often completely absent in susceptible genotypes.…”

Section: Regions Of High Svmentioning

confidence: 99%

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

et al. 2012

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Genome-wide structural and gene content variations are hypothesized to drive important phenotypic variation within a species. Structural and gene content variations were assessed among four soybean (Glycine max) genotypes using array hybridization and targeted resequencing. Many chromosomes exhibited relatively low rates of structural variation (SV) among genotypes. However, several regions exhibited both copy number and presence-absence variation, the most prominent found on chromosomes 3, 6, 7, 16, and 18. Interestingly, the regions most enriched for SV were specifically localized to gene-rich regions that harbor clustered multigene families. The most abundant classes of gene families associated with these regions were the nucleotide-binding and receptor-like protein classes, both of which are important for plant biotic defense. The colocalization of SV with plant defense response signal transduction pathways provides insight into the mechanisms of soybean resistance gene evolution and may inform the development of new approaches to resistance gene cloning.

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Identification of a large cluster of coiled coil-nucleotide binding site–leucine rich repeat-type genes from the Rps1 region containing Phytophthora resistance genes in soybean

Cited by 60 publications

References 47 publications

Excision of an Active CACTA-Like Transposable Element From DFR2 Causes Variegated Flowers in Soybean [Glycine max (L.) Merr.]

Excision of an Active CACTA-Like Transposable Element From DFR2 Causes Variegated Flowers in Soybean [Glycine max (L.) Merr.]

Meiosis-Driven Genome Variation in Plants

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

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