Mapping of Phenotypic and Gene Expression QTL Related to Preharvest Sprouting and Seed Dormancy in White Winter Wheat PDF Download
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Author: Jesse David Munkvold
Publisher:
ISBN:
Category :
Languages : en
Pages : 300
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Author: Jesse David Munkvold
Publisher:
ISBN:
Category :
Languages : en
Pages : 300
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Author: Suthasinee Somyong
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Wheat preharvest sprouting (PHS) occurs when grain germinates on the plant before harvest, resulting in reduced grain quality. Previous mapping of quantitative trait loci (QTL) revealed a major PHS QTL located on chromosome 2B.1 that was significant in 16 environments and explained from 5 to 31% of the phenotypic variation. The objective of this project was to fine map the PHS QTL interval on 2B.1. For fine mapping the QTL interval, ESTs (expressed sequence tags) and comparative mapping were used to design 278 primer pairs, of which 22 produced polymorphic amplicons that mapped to the group 2 chromosomes. Fourteen mapped to chromosome 2B but only 10 were located in the QTL interval. Recombinant backcross populations (BC1F4 and BC1F5) were developed by backcrossing selected double haploids to a recurrent parent and selfing to the F4 and F5 generations. In each generation, three markers in the PHS QTL interval were used to screen for recombinants. Comparative analysis revealed good macrocollinearity between the PHS interval and a 3 million base pair (mb) region in rice chromosomes 7 and 3, and a 2.5 mb region in Brachypodium Super_0. Fine mapping revealed that the 2B.1 PHS QTL interval contained 2 PHS QTLs. The first PHS QTL, located between Wmc453c and Barc55, contributed one third of phenotypic variation and collocated with the seed dormancy QTL. The second PHS QTL, between Wmc474 and rCaPK, contributed two thirds of the variation. The PHS resistance alleles were contributed from Cayuga parent. One of the PHS Cayuga resistance alleles originated in Golden Chief, a parent of Clark's Cream. One of the candidate genes, Calmodulin/Ca2+ dependent protein kinase, linked with one PHS QTL. Although many recombinant families were identified, the lack of polymorphism for markers in the QTL interval prevented the localization of the recombination breakpoints and identification of the gene underlying the phenotype.
Author: Mingqin Shao
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Wheat yield and quality is influenced by many abiotic and biotic environmental factors. Pre-harvest sprouting (PHS) occurs when physiologically matured spikes are exposed to wet field conditions before harvest, which results in seed germination and causes significant losses in yield and end-use quality. Wheat stripe rust is one of the most important biotic factors reducing grain yield and quality. To investigate the genetic basis of the resistance to PHS and stripe rust in hard white winter wheat cultivars Danby and Tiger and develop molecular markers for marker- assisted breeding, a double haploid (DH) population, derived from those two cultivars, was genotyped with simple sequence repeats (SSR) markers and simple nucleotide polymorphism (SNP) markers. This DH population was assessed for resistance to PHS and stripe rust in both greenhouse and field experiments. For PHS, one major resistant quantitative trait locus (QTL) was consistently detected on the short arm of chromosome 3A in all three experiments conducted and explained 21.6% to 41.0% of the phenotypic variation (PVE). This QTL is corresponding to a previously cloned gene, TaPHS1. A SNP in the promoter of TaPHS1 co- segregated with PHS resistance in this mapping population. Meanwhile, two other QTLs, Qphs.hwwg-3B.1 and Qphs.hwwg-5A.1, were consistently detected on the chromosome arms 3BS and 5AL in two experiments. These two QTLs showed significant additive effects with TaPHS1 in improving PHS resistance. For stripe rust, three major QTLs were consistently detected in four out of six environments for infection type (IT) or disease severity (DS). Two of them, QYr.hwwg-2AS1 and QYr.hwwg-4BL1, contributed by the Danby allele explained up to 28.4% of PVE for IT and 60.5% of PVE for DS. The third QTL, QYr.hwwg-3BS1, contributed by the Tiger allele, had PVE values up to 14.7% for IT and 22.9% for DS. QYr.hwwg-2AS1 and QYr.hwwg- 4BL1 are likely the same resistance genes reported previously on chromosome arms 2AS and 4BL. However, QYr.hwwg-3BS1 might be different from the reported gene cluster near the distal end of 3BS where Yr57, Yr4, Yr30 and Sr2 were located. Significant additive effects on reducing IT and DS were observed among these three major QTLs. In order to pyramid multiple QTLs in breeding, user-friendly Kompetitive allele specific PCR (KASP) markers were successfully developed for several QTLs identified in this study. The QTLs and their interactions found in this study together with those novel flanking KASP markers developed will be useful not only for understanding genetic mechanisms of PHS and stripe rust resistance but also for marker- assisted breeding to improve wheat resistance to PHS and stripe rust by gene pyramiding.
Author:
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ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 924
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Author: Shantel Amealia Martinez
Publisher:
ISBN:
Category : Wheat
Languages : en
Pages : 232
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Preharvest sprouting (PHS), germination of mature grain while still on the mother plant, occurs when conditions become cool and wet before harvest. The hydrolytic enzyme ?-amylase, induced during germination, mobilizes starch into simple carbohydrates to fuel seedling growth. Because this enzyme activity in flour causes poor end-use quality, sprouted grain sells at a severe discount. The falling number (FN) test measures ?-amylase activity in wheat meal or flour in the wheat industry. Seed dormancy, the inability to germinate even under favorable conditions, contributes about 60--80 % of genetic PHS tolerance. Red wheat varieties have higher seed dormancy and PHS tolerance than white. To improve white wheat, a genome-wide association study (GWAS) examined the genetic architecture of PHS tolerance in 469 soft white winter wheat accessions. Based on FN after natural or artificial rain, the GWAS identified 9 QTL (QFN.wsu), of which 4 co-localized with known PHS QTL and 3 with known FN/quality QTL. Based on visible sprout in spike-wetting tests, the GWAS identified 34 QTL (QPHS.wsu), of which 19 co-localized with known PHS loci and genes such as MOTHER OF FLOWERING TIME (TaMFT) and mitogen-activated protein kinase kinase 3 (TaMKK3-A). PHS tolerance in white wheat can result from higher sensitivity to the seed dormancy-inducing hormone abscisic acid (ABA). Enhanced Response to ABA (ERA8 ) is a semi-dominant ABA hypersensitive mutant, resulting in increased seed dormancy and PHS tolerance in the soft white spring wheat 'Zak'. The ERA8 locus was mapped to a large region of chromosome 4A relative to mutagen-induced SNPs in a Zak/ZakERA8 backcross population using bulk segregant analysis (BSA) of exome sequence from BC 3F2:3 wild-type and mutant DNA. Fine mapping using mutagen-induced SNPs in additional backcross lines localized ERA8 to a 4.5 Mb region containing 70 predicted genes. The only mutagen-induced coding region mutation strongly linked to ERA8 (LOD 16.51) resulted in a missense mutation in MKK3-A, a gene involved in Arabidopsis ABA signaling. Natural variation in wheat and barley MKK3 was previously shown to control seed dormancy and PHS tolerance.
Author: Chengdao Li
Publisher: Frontiers Media SA
ISBN: 2889457621
Category :
Languages : en
Pages : 235
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Pre-harvest sprouting (PHS) and late-maturity alpha-amylase (LMA) are two of the biggest grain quality defects that grain growers encounter. About 50 percent of the global wheat crop is affected by pre-harvest sprouting to various degrees. Pre-harvest sprouting is a genetically-based quality defect and results in the presence of alpha-amylase in otherwise sound mature grain. It can range from perhaps undetectable to severe damage on grain and is measured by the falling numbers or alpha-amylase activity. This is an international issue, with sprouting damage lowering the value of crops to growers, seed and grain merchants, millers, maltsters, bakers, other processors, and ultimately the consumer. As such it has attracted attention from researchers in many biological and non-biological disciplines. The 13th International Symposium on Pre-Harvest Sprouting in Cereals was held 18-20 September, 2016 in Perth to discuss current findings of grain physiology, genetic pathways, trait expression and screening methods related to pre-harvest sprouting and LMA. This event followed the previous symposium in 2012 in Canada.
Author: Mian Abdur Rehman Arif
Publisher:
ISBN:
Category :
Languages : en
Pages : 388
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This study was undertaken to map quantitative trait loci (QTLs) and marker trait associations (MTAs) controlling seed longevity and dormancy in wheat using one bi-parental and two association mapping populations. QTL analysis of bi-parental 'International Triticeae Mapping Initiative' population reproduced in two different seasons resulted in the identification of one major and nine minor QTLs for seed longevity. There was one major QTL for dormancy observed on chromosome 4AL. The location of this QTL does not match with any of the longevity QTLs. One set of 96 winter wheat accessions (advanced gemplasm collection) and one set of 183 accessions consisting of a mixture of spring and winter wheat (genebank collection) revealed 73 and 340 MTAs for seed longevity, respectively. Of the 340 MTAs, 134 MTAs were observed after long term cold storage but the others after experimental ageing in genebank collection. The associations were distributed over all the wheat chromosomes except 4D which was not covered with markers. Results obtained after long term cold storage and experimental ageing did match only to some extent in this study which could be due to different quality of seeds produced during different seasons. However, it also can be proposed that different mechanisms are involved during deterioration in cold storage over long periods and decaying during artificial ageing treatments. For dormancy, there were 68 and 118 MTAs identified in the advanced germplasm collection and genebank collection, respectively, in addition to one major QTL on chromosome 4A in the ITMI population. Similarly, pre-harvest sprouting revealed 32 and 193 MTAs in case of advanced germplasm collection and genebank accessions, respectively. Co-linearity was found among wheat, rice and barley for loci influencing dormancy and PHS.
Author: Christy A. McCarthy
Publisher:
ISBN:
Category : Soft wheat
Languages : en
Pages : 307
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Wheat (Triticum aestivum) is a highly valuable crop that makes up a large portion of the world’s food. However, breeding for improved varieties with desirable characteristics can be a challenge. This research examined two different issues wheat breeders deal with throughout the selection process all the way to production of Certified seed. The first study examined how 39 cultivars as well as 6 experimental crosses differ in grain dormancy expression. In order to see if dormancy has been systematically bred out of soft white winter wheat, the release date of the cultivars used in this trial ranged from 1948 to 2012. The second study investigated the source of phenotypic variation that appeared in Foundation seed fields of the recently released variety Bobtail. Bobtail was bred to be a semi-dwarf awnletted wheat that was superior in productivity and disease resistance. Plants of Bobtail were observed to segregate for awned and awnless phenotypes which also varied in plant height. Since there was variation in plant phenotypes observed in the Foundation seed field, it was important to determine what was causing the plant segregation. The first study was conducted over the course of two years and in the first year was only planted at Corvallis, OR, while second year trials were planted at Corvallis, OR as well as Pendleton, OR. To investigate how varieties differed in dormancy expression, seed germination trials were conducted at two temperatures in the first year (4°C and 20°C), and four temperatures in the second year (4°C, 10°C, 20°C and 30°C). In the first year, the impact of temperature during seed germination as well as dry storage on the breakdown of grain dormancy expression was investigated; whereas in the second year, the effects of ripening environment and temperature during germination on dormancy expression were determined. First year results demonstrated that soft white winter wheat does not show any grain dormancy at 20°C within the first few weeks after harvest, regardless of the temperature in which the grain was stored or germinated. Results from the second year showed that grain ripening environment has an impact on seed germination rates at different temperatures. A rain event occurred two days prior to harvest at the Corvallis, OR location but not at the Pendleton, OR location. None of the varieties showed any dormancy when they were imbibed at 20°C within 48 hours after harvest. However, some varieties demonstrated high-temperature induced dormancy when they were imbibed and kept at 30°C. This temperature slowed seed germination rate and cultivars that exhibited high-temperature induced dormancy were: Brevor, Bobtail, Cayuga, Gene, Nugaines, Rely and the experimental line 11-225-6H. There was no trend linking older released varieties to higher levels of seed dormancy compared to more recently released varieties, indicating that seed dormancy has not been systematically bred out of soft white winter wheat over time. For the second study, sixteen heads were snapped from a segregating head row that originated from a Bobtail Foundation seed field (one seed head was lost in the field). The objective of this study was to determine if the phenotypic variation was due to a contamination event or if it was a genetic variant of the variety Bobtail. There were several possibilities that could have caused the phenotypic variation such as an epistatic event, translocations, out-crossing or some type of seed contamination. To determine the source, sixteen plants from each of the fifteen heads collected from the segregating head row were grown in a greenhouse over the course of two generations. DNA samples were taken from all of the plants from the first generation. Eleven markers that showed polymorphism among a diverse panel of wheat varieties from a previous study were used in this trial and seven of the markers showed amplification and success. The results showed that there was very little variation among the individuals in this trial. The greenhouse trial that was grown to observe the plant segregation patterns revealed that the segregating lines segregated at a 3:1 awnless:awned ratio. All plants that came from an awned plant remained awned and several of the lines remained completely awnless. The marker analysis demonstrated there was no source of contamination and that plants observed segregating were a true genetic variant of the variety Bobtail. Phenotypic data showed that complete elimination of awned plants through the breeding and selection process had not occurred. Plants that came from segregating lines followed a typical Medelian segregation ratio. With this information, this variant was added to Bobtail’s variety description since it was not genotypically different.
Author: Meng Lin
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Wheat pre-harvest sprouting (PHS), germination of physiologically matured grains in a wheat spike before harvesting, can cause significant reduction in grain yield and end-use quality. Many quantitative trait loci (QTL) for PHS resistance have been reported in different sources. To determine the genetic architecture of PHS resistance and its relationship with grain color (GC) in US hard winter wheat, a genome-wide association study (GWAS) on both PHS resistance and GC was conducted using in a panel of 185 U.S. elite breeding lines and cultivars and 90K wheat SNP arrrays. PHS resistance was assessed by evaluating sprouting rates in wheat spikes harvested from both greenhouse and field experiments. Thirteen QTLs for PHS resistance were identified on 11 chromosomes in at least two experiments, and the effects of these QTLs varied among different environments. The common QTLs for PHS resistance and GC were identified on the long arms of the chromosome 3A and 3D, indicating pleiotropic effect of the two QTLs. Significant QTLs were also detected on chromosome arms 3AS and 4AL, which were not related to GC, suggesting that it is possible to improve PHS resistance in white wheat. To identify markers closely linked to the 4AL QTL, genotyping-by-sequencing (GBS) technology was used to analyze a population of recombinant inbred lines (RILs) developed from a cross between two parents, "Tutoumai A" and "Siyang 936", contrasting in 4AL QTL. Several closely linked GBS SNP markers to the 4AL QTL were identified and some of them were coverted to KASP for marker-assisted breeding. To investigate effects of the two non-GC related QTLs on 3AS and 4AL, both QTLs were transferered from "Tutoumai A" and "AUS1408" into a susceptible US hard winter wheat breeding line, NW97S186, through marker-assisted backcrossing using the gene marker TaPHS1 for 3AS QTL and a tightly linked KASP marker we developed for 4AL QTL. The 3AS QTL (TaPHS1) significantly interacted with environments and genetic backgrounds, whereas 4AL QTL (TaMKK3-A) interacted with environments only. The two QTLs showed additive effects on PHS resistance, indicating pyramiding these two QTLs can increase PHS resistance. To improve breeding selection efficiency, genomic prediction using genome-wide markers and marker-based prediction (MBP) using selected trait-linked markers were conducted in the association panel. Among the four genomic prediction methods evaluated, the ridge regression best linear unbiased prediction (rrBLUP) provides the best prediction among the tested methods (rrBLUP, BayesB, BayesC and BayesC0). However, MBP using 11 significant SNPs identified in the association study provides a better prediction than genomic prediction. Therefore, for traits that are controlled by a few major QTLs, MBP may be more effective than genomic selection.
Author: Andrew Hoffman Paterson
Publisher:
ISBN:
Category : Germination
Languages : en
Pages : 360
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