Variation of GmIRCHS (Glycine max inverted-repeat CHS pseudogene) is related to tolerance of low temperature-induced seed coat discoloration in yellow soybean

Ohnishi, Shin−ichi; Funatsuki, Hideyuki; Kasai, Atsushi; Kurauchi, Tasuku; Yamaguchi, Naoya; Takeuchi, Tōru; Yamazaki, Hiroyuki; Kurosaki, Hideki; Shirai, Shigehisa; Miyoshi, Tomoaki; Horita, Harukuni; Senda, Mineo

doi:10.1007/s00122-010-1475-6

Cited by 24 publications

(45 citation statements)

References 29 publications

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“…Among them, gSCC1 and gSCC8 corresponding to the two SCC genes, G (Song et al, 2004) and I (Ohnishi et al, 2011), respectively, were mapped into two small regions of 52,279,678–52,646,512 and 8,346,892–8,643,359 bp in NJRINP and 52,032,052–52,462,360 and 8,434,875–8,540,484 bp in NJRI4P on Chr. 01 and Chr.…”

Section: Resultsmentioning

confidence: 99%

“…Compared to the reference genome Wm82, the orders of most bins in each linkage map of NJRINP and NJRI4P showed good linear agreement with their physical positions. Using the two inter-specific maps, seven well-studied loci, B1 for SB (Chen and Shoemaker, 1998), G (Song et al, 2004) and I (Ohnishi et al, 2011) for SCC, and E2 (Watanabe et al, 2011), E3 (Watanabe et al, 2009), qDTF16.1 (Pooprompan et al, 2006) and two linked FLOWERING LOCUS T (Kong et al, 2010) for DTF, were detected, indicating the high quality of the two maps. The mapping accuracy was effectively improved, and few genes were contained in the 1-LOD interval of genes/QTLs.…”

Section: Discussionmentioning

confidence: 97%

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Characterizing Two Inter-specific Bin Maps for the Exploration of the QTLs/Genes that Confer Three Soybean Evolutionary Traits

et al. 2016

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Annual wild soybean (Glycine soja Sieb. and Zucc.), the wild progenitor of the cultivated soybean [Glycine max (L.) Merr.], is valuable for improving the later. The construction of a linkage map is crucial for studying the genetic differentiation between these species, but marker density is the main factor limiting the accuracy of such a map. Recent advances in next-generation sequencing technologies allow for the generation of high-density linkage maps. Here, two sets of inter-specific recombinant inbred line populations, named NJIRNP and NJIR4P, composed of 284 and 161 lines, respectively, were generated from the same wild male parent, PI 342618B, and genotyped by restriction-site-associated DNA sequencing. Two linkage maps containing 5,728 and 4,354 bins were constructed based on 89,680 and 80,995 single nucleotide polymorphisms, spanning a total genetic distance of 2204.6 and 2136.7 cM, with an average distance of 0.4 and 0.5 cM between neighboring bins in NJRINP and NJRI4P, respectively. With the two maps, seven well-studied loci, B1 for seed bloom; G and I for seed coat color; E2, E3, qDTF16.1 and two linked FLOWERING LOCUS T for days to flowering, were detected. In addition, two SB and two DTF loci were newly identified in wild soybean. Using two high-density maps, the mapping resolution was enhanced, e.g., G was narrowed to a region of 0.4 Mb on chromosome 1, encompassing 54 gene models, among which only Glyma01g40590 was predicted to be involved in anthocyanin accumulation, and its interaction with I was verified in both populations. In addition, five genes, Glyma16g03030, orthologous to Arabidopsis Phytochrome A (PHYA); Glyma13g28810, Glyma13g29920, and Glyma13g30710 predicted to encode the APETALA 2 (AP2) domain; and Glyma02g00300, involved in response to red or far red light, might be candidate DTF genes. Our results demonstrate that RAD-seq is a cost-effective approach for constructing high-density and high-quality bin maps that can be used to map QTLs/genes into such small enough regions that their candidate genes can be predicted.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 97%

Characterizing Two Inter-specific Bin Maps for the Exploration of the QTLs/Genes that Confer Three Soybean Evolutionary Traits

et al. 2016

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“…Therefore, a DNA marker has been sought to aid breeding of highly CD-tolerant cultivars. A quantitative trait locus (QTL) analysis suggested that GmASCHS , or another gene tightly linked to it, may be responsible for CD tolerance, and a DNA marker discriminating between GmIRCHS and GmASCHS can be useful for marker-assisted selection of CD-tolerant plants (Ohnishi et al 2011). However, variation of GmIRCHS genotypes cannot necessarily explain all CD phenotypes, suggesting the existence of other QTLs for CD tolerance.…”

Section: Full and Partial Seed Coat Pigmentation In Yellow Soybeanmentioning

confidence: 99%

“…However, variation of GmIRCHS genotypes cannot necessarily explain all CD phenotypes, suggesting the existence of other QTLs for CD tolerance. Indeed, a second QTL has been identified, which made a smaller contribution to CD tolerance than GmIRCHS (Ohnishi et al 2011). If other QTLs are detected and mapped precisely, more reliable marker-assisted selection of CD tolerance could be achieved by the combination of DNA markers for GmIRCHS and other QTLs.…”

Section: Full and Partial Seed Coat Pigmentation In Yellow Soybeanmentioning

confidence: 99%

Suppressive mechanism of seed coat pigmentation in yellow soybean

et al. 2012

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In soybean seeds, numerous variations in colors and pigmentation patterns exist, most of which are observed in the seed coat. Patterns of seed coat pigmentation are determined by four alleles (I, ii, ik and i) of the classically defined I locus, which controls the spatial distribution of anthocyanins and proanthocyanidins in the seed coat. Most commercial soybean cultivars produce yellow seeds with yellow cotyledons and nonpigmented seed coats, which are important traits of high-quality seeds. Plants carrying the I or ii allele show complete inhibition of pigmentation in the seed coat or pigmentation only in the hilum, respectively, resulting in a yellow seed phenotype. Classical genetic analyses of the I locus were performed in the 1920s and 1930s but, until recently, the molecular mechanism by which the I locus regulated seed coat pigmentation remained unclear. In this review, we provide an overview of the molecular suppressive mechanism of seed coat pigmentation in yellow soybean, with the main focus on the effect of the I allele. In addition, we discuss seed coat pigmentation phenomena in yellow soybean and their relationship to inhibition of I allele action.

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“…Chilling temperatures can also negatively affect seed appearance; for example, by causing seed coat discoloration and concomitant seed coat cracking (Funatsuki and Ohnishi 2009, Morrison et al 1998, Srinivasan and Arihara 1994, Takahashi and Abe 1994, 1999). A selection method for breeding soybeans tolerant to seed coat discoloration has been developed (Yumoto and Sasaki 1991), and the mechanism underlying seed coat discoloration has been clarified (Kasai et al 2009, Ohnishi et al 2011, Senda et al 2013). …”

Section: Introductionmentioning

confidence: 99%

Method for selection of soybeans tolerant to seed cracking under chilling temperatures

et al. 2014

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In Hokkaido, northern Japan, soybean [Glycine max (L.) Merr.] crops are damaged by cold weather. Chilling temperatures result in the appearance of cracking seeds (CS) in soybean crops, especially those grown in eastern and northern Hokkaido. Seed coats of CS are severely split on the dorsal side, and the cotyledons are exposed and frequently separated. CS occurrence causes unstable production because these seeds have no commodity value. However, little is known about the CS phenomenon. The aims of this study were to identify the cold-sensitive stage associated with CS occurrence and to develop a method to select CS-tolerant lines. First, we examined the relationship between chilling temperatures after flowering and CS occurrence in field tests. The average temperature 14 to 21 days after flowering was negatively correlated with the rate of CS. Second, we evaluated differences in CS tolerance among soybean cultivars and breeding lines in field tests. ‘Toyohomare’ and ‘Toiku-238’ were more CS-tolerant than ‘Yukihomare’ and ‘Toyomusume’. Third, we developed a selection method in which plants were subjected to 21-day chilling-temperature treatment from 10 days after flowering in a phytotron. This enabled comparisons of CS tolerance among cultivars. This selection method will be useful for breeding CS-tolerant soybeans.

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Variation of GmIRCHS (Glycine max inverted-repeat CHS pseudogene) is related to tolerance of low temperature-induced seed coat discoloration in yellow soybean

Cited by 24 publications

References 29 publications

Characterizing Two Inter-specific Bin Maps for the Exploration of the QTLs/Genes that Confer Three Soybean Evolutionary Traits

Characterizing Two Inter-specific Bin Maps for the Exploration of the QTLs/Genes that Confer Three Soybean Evolutionary Traits

Suppressive mechanism of seed coat pigmentation in yellow soybean

Method for selection of soybeans tolerant to seed cracking under chilling temperatures

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