Identification of loci for pre-harvest sprouting resistance in the highly dormant spring wheat RL4137

Liton, M M Uzzal Ahmed; McCartney, Curt A.; Hiebert, Colin W.; Kumar, Santosh; Jordan, Mark C.; Ayele, Belay T.

doi:10.1007/s00122-020-03685-y

Cited by 15 publications

(20 citation statements)

References 51 publications

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“…Although quite a few QTL for wheat PHS resistance on chromosome 4A have also been reported (Kato et al, 2001;Mares et al, 2005;Torada et al, 2005;Imtiaz et al, 2008;Rasul et al, 2009;Singh et al, 2010;Kulwal et al, 2012;Cabral et al, 2014;Jiang et al, 2015;Cao et al, 2016;Zhou et al, 2017;Martinez et al, 2018;Zuo et al, 2019;Liton et al, 2021), Qphs.caas-4AL appears to be unique based on genetic mapping and physical locations of the flanking SNPs according to IWGSC RefSeq 1.0 (Supplementary Table 9). QTL pyramiding plays an important role in breeding, and resistance allele combinations of QTL for PHS have been reported previously (Imtiaz et al, 2008;Shao et al, 2018;Liton et al, 2021). In this study, we identified that the RILs combining resistance alleles in Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-4AL had the lowest GI (Figure 2).…”

Section: Qphscaas-4al Has Potential Value For Wheat Breedingmentioning

confidence: 99%

Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

Zhang

et al. 2021

Front. Plant Sci.

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Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6–18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D, respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection.

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Section: Qphscaas-4al Has Potential Value For Wheat Breedingmentioning

confidence: 99%

Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

Zhang

et al. 2021

Front. Plant Sci.

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“…The permanent nature also makes a DH population efficient for QTL analysis (Liton et al. 2020). Despite the low sporophyte occurrence ratio, we may obtain more normal sporophytes of each DH line by inoculating larger biomass of gametophytes according to our purpose in practice.…”

Section: Discussionmentioning

confidence: 99%

“…The use of "male" and "female" sporophytes as the parents for cross has an advantage in breeding practice as the spores are able to attach the seedling strings more steadily than their gametophyte counterparts, thereby avoiding detachment of gametophytes and young seedlings (Shan et al 2013, Li et al 2017). The permanent nature also makes a DH population efficient for QTL analysis (Liton et al 2020). Despite the low sporophyte occurrence ratio, we may obtain more normal sporophytes of each DH line by inoculating larger biomass of gametophytes according to our purpose in practice.…”

Section: Inheritance Of Monoecy and Parthenogenesismentioning

confidence: 99%

“…A DH population is a kind of mapping population that has been widely used for construction of genetic linkage maps and linkage map‐based analyses of quantitative trait loci (QTLs; Liton et al. 2020, Ren et al. 2020, Ye et al.…”

mentioning

confidence: 99%

“…The DH line is homozygous at all loci and thus is completely inbred. A DH population is a kind of mapping population that has been widely used for construction of genetic linkage maps and linkage map-based analyses of quantitative trait loci (QTLs; Liton et al 2020, Ren et al 2020, Ye et al 2020, Yuan et al 2020. It is especially useful for QTL analyses across different time and environments (Forster et al 2007).…”

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confidence: 99%

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The Inheritable Characteristics of Monoecy and Parthenogenesis Provide A Means for Establishing A Doubled Haploid Population in the Economically Important Brown Alga Undariapinnatifida (Laminariales, Alariaceae)

Shan

Pang

Wang

et al. 2021

Journal of Phycology

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Monoecy and parthenogenesis exist in certain male and female gametophytes of the brown alga Undaria pinnatifida. The inheritance of these traits is not known. In this study, we made a cross between a male and a female gametophyte clone which could exhibit monoecy and parthenogenesis phenotypes, respectively, and obtained their next‐generation gametophyte offspring. We found that under conditions suitable for gametogenesis, all of the male offspring (n = 100) exhibited monoecy phenotype and all of the female offspring (n = 100) only formed oogonia and underwent parthenogenesis, suggesting that monoecy and parthenogenesis phenotypes are inheritable. Then, we established a doubled haploid (DH) population through monoecious selfing and parthenogenesis, and evaluated the young sporophyte growth and the maximum quantum yield (Fv/Fm) of 10 “male” and 10 “female” DH lines. On day 60, the average length of the “male” DH lines was significantly larger than that of the “female” DH lines, while their average Fv/Fm values were not significantly different. Monoecious selfing seemed superior to parthenogenesis as the sporophyte formation efficiency, and the young sporophyte growth was better in the former than in the latter. We also crossed two monoecious gametophytes with another male gametophyte, and a parentage analysis showed success of obtaining hybrid sporophytes, indicating that the female gametes released by the monoecious gametophyte can actually be fertilized by sperm. The approach of establishing a DH population proposed here will be useful in genetic breeding and quantitative trait loci mapping in U. pinnatifida and may be applicable to other kelp species.

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Genome‐wide association mapping for pre‐harvest sprouting in European winter wheat detects novel resistance QTL, pleiotropic effects, and structural variation in multiple genomes

Dallinger

Löschenberger²,

Azrak³

et al. 2023

The Plant Genome

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Pre‐harvest sprouting (PHS), germination of seeds before harvest, is a major problem in global wheat (Triticum aestivum L.) production, and leads to reduced bread‐making quality in affected grain. Breeding for PHS resistance can prevent losses under adverse conditions. Selecting resistant lines in years lacking pre‐harvest rain, requires challenging of plants in the field or in the laboratory or using genetic markers. Despite the availability of a wheat reference and pan‐genome, linking markers, genes, allelic, and structural variation, a complete understanding of the mechanisms underlying various sources of PHS resistance is still lacking. Therefore, we challenged a population of European wheat varieties and breeding lines with PHS conditions and phenotyped them for PHS traits, grain quality, phenological and agronomic traits to conduct genome‐wide association mapping. Furthermore, we compared these marker‐trait associations to previously reported PHS loci and evaluated their usefulness for breeding. We found markers associated with PHS on all chromosomes, with strong evidence for novel quantitative trait locus/loci (QTL) on chromosome 1A and 5B. The QTL on chromosome 1A lacks pleiotropic effect, for the QTL on 5B we detected pleiotropic effects on phenology and grain quality. Multiple peaks on chromosome 4A co‐located with the major resistance locus Phs‐A1, for which two causal genes, TaPM19 and TaMKK3, have been proposed. Mapping markers and genes to the pan‐genome and chromosomal alignments provide evidence for structural variation around this major PHS‐resistance locus. Although PHS is controlled by many loci distributed across the wheat genome, Phs‐A1 on chromosome 4A seems to be the most effective and widely deployed source of resistance, in European wheat varieties.

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Identification of loci for pre-harvest sprouting resistance in the highly dormant spring wheat RL4137

Cited by 15 publications

References 51 publications

Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

The Inheritable Characteristics of Monoecy and Parthenogenesis Provide A Means for Establishing A Doubled Haploid Population in the Economically Important Brown Alga Undariapinnatifida (Laminariales, Alariaceae)

Genome‐wide association mapping for pre‐harvest sprouting in European winter wheat detects novel resistance QTL, pleiotropic effects, and structural variation in multiple genomes

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