Identification of Quantitative Trait Loci Underlying Kernel Extra-softness and Related Traits by Linkage and Association Mapping in Wheat (Triticum Aestivum L.) PDF Download
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Author: Guomei Wang
Publisher:
ISBN:
Category : Soft wheat
Languages : en
Pages : 160
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Book Description
Kernel hardness (KHA) is a major factor determining break flour yield (BFY) and end-use quality of common wheat (Triticum aestivum L.). Within the soft wheat class, genotypes with consistently softer grains than common soft wheat are considered to be 'extra-soft'. In addition, 'extra-soft' wheats have greater BFY than common soft wheat lines. In order to better understand this interrelationship, a set of 164 F6-recombinant inbred lines (RILs) developed from a soft x 'extra-soft' wheat cross was evaluated for KHA, BFY, and other related traits in six field environments. The estimates of broad-sense heritability for KHA and BFY ranged from 0.84 to 0.96 and 0.56 to 0.76, respectively. Significant environmental effects and genotype by environment interactions were detected for all traits evaluated. A comprehensive genetic linkage map was created with 650 molecular markers based on this mapping population. Three chromosome translocations, 1BL. 1RS, 2N^S-2AS. 2AL and 5B:7B, were identified during linkage analysis. A total of 47 quantitative trait loci (QTL) were identified for nine traits including KHA, BFY, bran yield (BRN), unground middling yield (MID), plant height (PHT), days to heading (HDD), thousand-kernel weight (TKW), grain protein content (GPC), and test weight (TWT). The number of QTL per trait ranged from three for MID to nine for GPC. The phenotypic variance explained by individual QTL ranged from 5.8 to 47.6%. Among five QTL identified for KHA, the two most important QTL were located on chromosomes 4DS (Xbarc1118-Rht-D1 interval) and 4BS (Xwmc617-Rht-B1 interval), indicating that the 'extra-soft' characteristic was not controlled by the 5DS Hardness (Ha) locus which encodes the two puroindoline genes pinA and pinB. The co-location of QTL for KHA, BFY, BRN, and MID on 4DS suggested that genetic factors affecting KHA may have a pleiotropic effect on BFY. Two co-located QTL for TWT, TKW and PHT were detected on 4DS and 4BS, and a QTL for HDD was detected on 4DS, indicating that these QTL may represent the consequence of the semi-dwarfing green-revolution genes Rht-D1 and Rht-B1 located on 4DS and 4BS, respectively. Additional analysis suggested that the QTL for KHA on 4DS and 4BS are the effects of genes linked to Rht-D1 and Rht-B1, rather than pleiotropic effects of these genes. Some coincident QTL for the traits that were evaluated represent the interrelationships of phenotypic traits, where both KHA and BFY were associated with HDD and TWT based on path coefficient analysis. Association mapping can be an effective means for identifying, validating, and fine mapping genes and QTL in crop plants. To test this approach, a set of 94 diverse elite wheat lines was phenotyped for five important traits and genotyped with 487 molecular markers. In this study, the marker-trait association analysis showed that the gene pinB (Ha locus) was significantly associated with KHA as it is known to define the difference between soft and hard wheat classes. Additionally, the significant associations of marker XwPt-7187 with KHA, XwPt-1250 and XwPt-4628 with TWT, and Xgwm512 with PHT mark the first report of such associations in these genomic regions. This study, aiming at the genetic dissection of wheat kernel extra-softness and related traits, enhanced our understanding of both genetic control of and environmental effects on these important traits. Path coefficient analysis showed the promise of an alternative phenotypic selection approach that is more cost effective than direct measurement of kernel quality. Three chromosome translocations were discovered and their approximate chromosome break points were located. Numerous QTL were identified for these important traits. The major QTL can serve as a start point for fine mapping that eventually lead to the cloning of the QTL through map-based or candidate gene approach. Association mapping, as an alternate approach and complementary tool to QTL mapping, was demonstrated feasible in wheat for identification of marker-trait associations and cross validation of QTL or genes identified from bi-parent mapping populations.
Author: Guomei Wang
Publisher:
ISBN:
Category : Soft wheat
Languages : en
Pages : 160
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Book Description
Kernel hardness (KHA) is a major factor determining break flour yield (BFY) and end-use quality of common wheat (Triticum aestivum L.). Within the soft wheat class, genotypes with consistently softer grains than common soft wheat are considered to be 'extra-soft'. In addition, 'extra-soft' wheats have greater BFY than common soft wheat lines. In order to better understand this interrelationship, a set of 164 F6-recombinant inbred lines (RILs) developed from a soft x 'extra-soft' wheat cross was evaluated for KHA, BFY, and other related traits in six field environments. The estimates of broad-sense heritability for KHA and BFY ranged from 0.84 to 0.96 and 0.56 to 0.76, respectively. Significant environmental effects and genotype by environment interactions were detected for all traits evaluated. A comprehensive genetic linkage map was created with 650 molecular markers based on this mapping population. Three chromosome translocations, 1BL. 1RS, 2N^S-2AS. 2AL and 5B:7B, were identified during linkage analysis. A total of 47 quantitative trait loci (QTL) were identified for nine traits including KHA, BFY, bran yield (BRN), unground middling yield (MID), plant height (PHT), days to heading (HDD), thousand-kernel weight (TKW), grain protein content (GPC), and test weight (TWT). The number of QTL per trait ranged from three for MID to nine for GPC. The phenotypic variance explained by individual QTL ranged from 5.8 to 47.6%. Among five QTL identified for KHA, the two most important QTL were located on chromosomes 4DS (Xbarc1118-Rht-D1 interval) and 4BS (Xwmc617-Rht-B1 interval), indicating that the 'extra-soft' characteristic was not controlled by the 5DS Hardness (Ha) locus which encodes the two puroindoline genes pinA and pinB. The co-location of QTL for KHA, BFY, BRN, and MID on 4DS suggested that genetic factors affecting KHA may have a pleiotropic effect on BFY. Two co-located QTL for TWT, TKW and PHT were detected on 4DS and 4BS, and a QTL for HDD was detected on 4DS, indicating that these QTL may represent the consequence of the semi-dwarfing green-revolution genes Rht-D1 and Rht-B1 located on 4DS and 4BS, respectively. Additional analysis suggested that the QTL for KHA on 4DS and 4BS are the effects of genes linked to Rht-D1 and Rht-B1, rather than pleiotropic effects of these genes. Some coincident QTL for the traits that were evaluated represent the interrelationships of phenotypic traits, where both KHA and BFY were associated with HDD and TWT based on path coefficient analysis. Association mapping can be an effective means for identifying, validating, and fine mapping genes and QTL in crop plants. To test this approach, a set of 94 diverse elite wheat lines was phenotyped for five important traits and genotyped with 487 molecular markers. In this study, the marker-trait association analysis showed that the gene pinB (Ha locus) was significantly associated with KHA as it is known to define the difference between soft and hard wheat classes. Additionally, the significant associations of marker XwPt-7187 with KHA, XwPt-1250 and XwPt-4628 with TWT, and Xgwm512 with PHT mark the first report of such associations in these genomic regions. This study, aiming at the genetic dissection of wheat kernel extra-softness and related traits, enhanced our understanding of both genetic control of and environmental effects on these important traits. Path coefficient analysis showed the promise of an alternative phenotypic selection approach that is more cost effective than direct measurement of kernel quality. Three chromosome translocations were discovered and their approximate chromosome break points were located. Numerous QTL were identified for these important traits. The major QTL can serve as a start point for fine mapping that eventually lead to the cloning of the QTL through map-based or candidate gene approach. Association mapping, as an alternate approach and complementary tool to QTL mapping, was demonstrated feasible in wheat for identification of marker-trait associations and cross validation of QTL or genes identified from bi-parent mapping populations.
Author: Kendra Lyn Gregory Jernigan
Publisher:
ISBN:
Category :
Languages : en
Pages : 158
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Book Description
Wheat (Triticum aestivum L.) is used in diverse baked products that require specific end use quality traits. Kernel texture, flour water absorption capacity, gluten strength, starch composition, and other flour constituents all influence overall flour functionality and dough rheology, specifying both wheat market class and intended end product. Wheat breeders need to develop cultivars with superior end-use quality traits, while also optimizing important agronomic traits. Our first objective was to use a genetic linkage map and 207 recombinant inbred lines (RIL) from a soft white 'Coda' by 'Brundage' cross to identify quantitative trait loci (QTL) for grain, milling, and baking traits. The linkage map was developed using 570 single nucleotide polymorphisms (SNP) and 136 simple sequence repeat markers. The RILs were grown in five locations in Idaho and Washington from 2006 to 2013. We detected three QTL on chromosomes 2D, 4B, and 6B that were consistently associated with multiple end-use quality traits. Our second objective was to use a genetic linkage map and 131 RILs from a soft white 'Louise' by 'Alpowa' cross to identify QTL associated with arabinoxylan content and milling traits. The linkage map consisted of 924 SNPs and 41 linkage groups. This population was grown in three Washington locations from 2011 to 2012. We detected 28 QTL associated with seven arabinoxylan content and milling traits. Our third objective was to use 480 advanced breeding lines and Pacific Northwest cultivars to identify molecular markers associated with 21 end-use quality traits. Genotypic data from the iSelect 90K SNP chip was combined with best linear unbiased predictions of historic phenotypic data from the USDA-ARS Western Wheat Quality Laboratory. Genome-wide association mapping in the R package, genome association and prediction integrated tool (GAPIT), detected significant markers for multiple end-use quality traits on chromosomes1B, 1D, 2D, 5A, 5B, and 7A. An improved understanding of the genetic architecture underlying end-use quality traits in wheat may assist breeders with cultivar development for superior end-use quality, particularly by increasing frequencies of favorable alleles in breeding populations. Cultivars with superior end-use quality will allow US wheat producers to maintain domestic and international markets.
Author: Nicola J. Camp
Publisher: Springer Science & Business Media
ISBN: 1592591760
Category : Medical
Languages : en
Pages : 362
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Book Description
In Quantitative Trait Loci: Methods and Protocols, a panel of highly experienced statistical geneticists demonstrate in a step-by-step fashion how to successfully analyze quantitative trait data using a variety of methods and software for the detection and fine mapping of quantitative trait loci (QTL). Writing for the nonmathematician, these experts guide the investigator from the design stage of a project onwards, providing detailed explanations of how best to proceed with each specific analysis, to find and use appropriate software, and to interpret results. Worked examples, citations to key papers, and variations in method ease the way to understanding and successful studies. Among the cutting-edge techniques presented are QTDT methods, variance components methods, and the Markov Chain Monte Carlo method for joint linkage and segregation analysis.
Author: Robert Christopher Gaynor
Publisher:
ISBN:
Category : Factor analysis
Languages : en
Pages : 170
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Book Description
Increasing grain yield in wheat (Triticum aestivum L.) is a challenging task, because yield is a complex trait controlled by many genes and highly influenced by environmental factors. The genetic control of yield components and other traits associated with yield may be less complex and thus more manageable for breeding. This study seeks to identify quantitative trait loci (QTLs) for these traits. Two new genetic linkage maps were constructed from recombinant inbred lines (RILs) derived from crosses between the Oregon soft white winter wheat variety Tubbs and a Western European hard red winter wheat variety, Einstein. A third linkage map was constructed from RILs from a cross with Tubbs and a Western European experimental hard red winter wheat line. A combination of Diversity Arrays Technology (DArT), Simple Sequence Repeat (SSR), orw5, and B1 markers were used to construct genetic linkage maps. Two replications of the RIL populations were grown in yield trial sized plots at Corvallis, OR and Pendleton, OR in 2009. The RILs were evaluated for grain yield, spikes per m2, fertile spikelets per spike, sterile spikelets per spike, seeds per spike, seeds per fertile spikelet, average seed weight, growing degree days (GDD) to flowering, GDD to physiological maturity, GDD of grain fill, plant height, test weight, and percent grain protein. Composite interval mapping (CIM) detected 146 QTLs for these traits spread across all chromosomes except for 6D. Thirty six percent of all of the QTLs detected were in close proximity to four loci: Rht-B1, Rht-D1, B1, and Xgwm372. The use of factor analysis to aid in QTL mapping for correlated traits related to spike morphology was explored. Quantitative trait loci mapping of factor scores for these traits potentially showed an increase in statistical power to detect QTLs and a decrease in the probability of type I error over mapping the traits individually.
Author:
Publisher:
ISBN:
Category :
Languages : pt-BR
Pages :
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Author: Joel Ira Weller
Publisher: CABI
ISBN: 1845937341
Category : Technology & Engineering
Languages : en
Pages : 288
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Book Description
Quantitative Trait Loci (QTL) is a topic of major agricultural significance for efficient livestock production. This book covers various statistical methods that have been used or proposed for detection and analysis of QTL and marker-and gene-assisted selection in animal genetics and breeding.
Author: Jeesun Jung
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
As a large number of single nucleotide polymorphisms (SNPs) and microsatellite markers are available, high resolution mapping employing multiple markers or multiple allele markers is an important step to identify quantitative trait locus (QTL) of complex human disease. For many complex diseases, quantitative phenotype values contain more information than dichotomous traits do. Much research has been done on conducting high resolution mapping using information of linkage and linkage disequilibrium. The most commonly employed approaches for mapping QTL are pedigree-based linkage analysis and population-based association analysis. As one of the methods dealing with multiple alleles markers, mixed models are developed to work out family-based association study with the information of transmitted allele and nontransmitted allele from one parent to offspring. For multiple markers, variance component models are proposed to perform association study and linkage analysis simultaneously. Linkage analysis provides suggestive linkage based on a broad chromosome region and is robust to population admixtures. One the other hand, allelic association due to linkage disequilibrium (LD) usually operates over very short genetic distance, but is affected by population stratification. Combining both approaches plays a synergistic role in overcoming their limitations and in increasing the efficiency and effectiveness of gene mapping.
Author: Khalil Zaynali Nezhad
Publisher:
ISBN:
Category :
Languages : en
Pages : 267
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Book Description
Two bread wheat (T. aestivum L.) accessions were selected as parental lines. Population genotyping was conducted on 143 F2 plants and phenotyping was carried out on 133 F2:3 families. The molecular genetic linkage map was constructed including 293 loci associated to 19 wheat chromosomes. There are 76 new loci compared to the ITMI map. The analysis revealed eight QTLs for days to flowering and seven QTLs for plant height. Five QTLs for spike length were identified. The QTL for seed length on chromosome 5B was mapped for all trait measurements under both conditions. The present study revealed four and six QTLs for thousand-grain weight under control and stress conditions, respectively. Only one QTL on chromosome 4BL was common for both conditions. Five QTLs for thousand-grain weight were found to be specific to stress condition on chromosomes 1B, 4AL, 7AS, and 7DS. Identifying QTLs for thousand-grain weight under post-anthesis drought stress on chromosomes 7DS, 7AS, and 4AL and considering the known reciprocal translocation of 4AL/7BS in wheat, revealed the importance of the chromosomes from the homoeologous group 7 of Triticeae.
Author: Matthew P. Reynolds
Publisher: CABI
ISBN: 1845936337
Category : Science
Languages : en
Pages : 310
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Book Description
Agricultural, botanical, and social scientists from the four quarters of the world address the impact of climate change on crop productivity, some approaches to adapt plants to both biotic and abiotic stresses, and measures to reduce greenhouse gases. They cover predictions of climate change within the context of agriculture, adapting to biotic and abiotic stresses through crop breeding, sustainable and resource-conserving technologies for adapting to and mitigating climate change, and new tools for enhancing crop adaptation to climate change. Specific topics include economic impacts of climate change on agriculture to 2030, breeding for adaptation to heat and drought stress, managing resident soil microbial community structure and function to suppress the development of soil-borne diseases, and applying geographical information systems (GIS) and crop simulation modeling in climate change research.
Author: Hua Chen
Publisher:
ISBN:
Category : Wheat
Languages : en
Pages : 168
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Book Description
Early maturity, grain yield and grain protein content are some of the important traits in western Canadian wheat breeding programs. A series of experiments were conducted to explore the genetic basis of days to heading, and maturity, plant height, grain protein, grain yield and related traits. In a spring wheat population of 187 recombinant inbred lines genotyped with 341 Diversity Array Technology (DArT) polymorphic markers, a total of 21 quantitative trait loci (QTLs) were identified for all phenotypic traits recorded, except plant height and grain protein content. Two earliness per se QTLs were mapped on chromosomes 1A (QEps.dms-1A) and 4A (QEps.dms-4A) in all three growing seasons, contributing 15-27% and 8-10%, respectively, to the total genetic variation in days to maturity. The two earliness QTLs and Vrn-B1 exhibited additive interaction. In the same population, lines carrying the resistant allele of Lr34/Yr18 were taller, matured earlier, yielded less grain with lower test weights than lines without Lr34/Yr18. Lines with Lr34/Yr18 also exhibited lower leaf and stripe rust infection than lines with the susceptible allele. The failure to combine Lr34/Yr18 with high yield, protein, and SDS sedimentation suggested single seed descent or doubled haploid populations for the combined selection of multiple quantitatively inherited traits, and simply one molecular marker, would require population sizes in excess of at least 500 to have any possibility of selection success. Genetic diversity analysis for earliness related and plant height reducing genes in 82 spring wheat cultivars registered in western Canada through eight diagnostic DNA markers suggested breeding efforts in western Canada have resulted in the incorporation of vernalization and photoperiod insensitive and height reducing genes in modern cultivars to promote early maturity, to make use of off-season nurseries in other parts of the world and to improve lodging tolerance. Using genome-wide association mapping (GWAS). we identified a total of 152 significant marker-trait associations; however, there were only 18 genomic regions that consisted of clusters of 3 to 20 significant single nucleotide polymorphisms (SNPs) across 12 chromosomes, including two regions each for grain yield, test weight and protein content, six regions for plant height and six other coincident regions that were associated with two or three traits. The genomic region associated with plant height on chromosome 4B showed high linkage disequilibrium (r2 > 0.80) with the semi-dwarfing gene Rht-B1. Results of these studies suggest that besides the widely used semi-dwarf and early maturity related genes, there is a wide spectrum of loci available that could be used for modulating plant height, days to maturity, grain yield and grain protein content in western Canadian wheat germplasm.
