Association mapping of sponge cake volume in U.S. Pacific Northwest elite soft white wheat (Triticum aestivum L.)

Thompson, Yvonne A.; Carter, Arron H.; Ward, Brian P.; Kiszonas, Alecia M.; Morris, Craig F.

doi:10.1016/j.jcs.2021.103250

Cited by 4 publications

(3 citation statements)

References 20 publications

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“…Nonetheless, the availability of mixed models that integrates the years and environments followed by estimating the mean genetic effects of individual inbred lines, such as best linear unbiased prediction ( Smith et al, 2005 ), made it possible to utilize such data sets in the marker-trait discovery via the GWAS analysis. As a result, the historically recorded unbalanced phenotypic datasets found in breeding programs have been successfully used to detect relevant QTLs and markers in different crops associated with traits such as yield, quality, and disease resistance ( Kraakman et al, 2004 ; Pozniak et al, 2012 ; Wang et al, 2012 ; Fiedler et al, 2017 ; Johnson et al, 2019 ; Liu et al, 2019 ; Thompson et al, 2021 ). In addition, the GS accuracy greatly improved when the models trained with populations comprised historical phenotypic datasets in breeding programs ( Dawson et al, 2013 ; Gapare et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

2022

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Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP). Marker-trait associations (MTAs) were conducted using 6902 quality single nucleotide polymorphism (SNP) markers generated from the diversity arrays technology sequencing (DArTseq) and Genotyping-by-sequencing (GBS) sequencing methods. The best linear unbiased prediction (BLUP) values were estimated from the two-decades-long (1999–2020) unbalanced phenotypic data sets recorded from two private breeding programs, the Findus and the Birds eye, now owned by Nomad Foods. Analysis of variance revealed a highly significant variation between genotypes and genotype-by-environment interactions for the ten traits. The genetic diversity and population structure analyses estimated an intermediate level of genetic variation with two optimal sub-groups within the current panel. A total of 48 significant (P < 0.0001) MTAs were identified for eight different traits, including five for wrinkled vining pea yield on chr2LG1, chr4LG4, chr7LG7, and scaffolds (two), and six for adult plant resistance to downy mildew on chr1LG6, chr3LG5 (two), chr6LG2, and chr7LG7 (two). We reported several novel MTAs for different crucial traits with agronomic importance in wrinkled vining pea production for the first time, and these candidate markers could be easily validated and integrated into the active breeding programs for marker-assisted selection.

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Section: Introductionmentioning

confidence: 99%

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

2022

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“…Since most end-use quality traits are predominantly controlled by genetic factors [ 3 – 5 ], a better understanding of the underlying genetic architecture of the various traits can support strategies for both phenotypic and genotypic selection, including an assessment of the potential effectiveness of marker-assisted selection. Analysis of marker trait associations have identified numerous quantitative trait loci (QTL) for different end-use quality traits distributed across all 21 wheat chromosomes [ 2 , 4 , 6 – 23 ]. However, most of these studies were performed in hard wheat (bread wheat) and these investigations [ 2 , 4 , 17 , 22 , 23 ] were performed in soft wheat.…”

Section: Introductionmentioning

confidence: 99%

“…Analysis of marker trait associations have identified numerous quantitative trait loci (QTL) for different end-use quality traits distributed across all 21 wheat chromosomes [ 2 , 4 , 6 – 23 ]. However, most of these studies were performed in hard wheat (bread wheat) and these investigations [ 2 , 4 , 17 , 22 , 23 ] were performed in soft wheat. Soft white wheat has unique milling and baking parameters which are aimed at making food products such as cookies and cakes [ 24 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic architecture of end-use quality traits in soft white winter wheat

et al. 2022

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Background Genetic improvement of end-use quality is an important objective in wheat breeding programs to meet the requirements of grain markets, millers, and bakers. However, end-use quality phenotyping is expensive and laborious thus, testing is often delayed until advanced generations. To better understand the underlying genetic architecture of end-use quality traits, we investigated the phenotypic and genotypic structure of 14 end-use quality traits in 672 advanced soft white winter wheat breeding lines and cultivars adapted to the Pacific Northwest region of the United States. Results This collection of germplasm had continuous distributions for the 14 end-use quality traits with industrially significant differences for all traits. The breeding lines and cultivars were genotyped using genotyping-by-sequencing and 40,518 SNP markers were used for association mapping (GWAS). The GWAS identified 178 marker-trait associations (MTAs) distributed across all wheat chromosomes. A total of 40 MTAs were positioned within genomic regions of previously discovered end-use quality genes/QTL. Among the identified MTAs, 12 markers had large effects and thus could be considered in the larger scheme of selecting and fixing favorable alleles in breeding for end-use quality in soft white wheat germplasm. We also identified 15 loci (two of them with large effects) that can be used for simultaneous breeding of more than a single end-use quality trait. The results highlight the complex nature of the genetic architecture of end-use quality, and the challenges of simultaneously selecting favorable genotypes for a large number of traits. This study also illustrates that some end-use quality traits were mainly controlled by a larger number of small-effect loci and may be more amenable to alternate selection strategies such as genomic selection. Conclusions In conclusion, a breeder may be faced with the dilemma of balancing genotypic selection in early generation(s) versus costly phenotyping later on.

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Effect of components and heating on rheological properties of custard

Nishida,

Watanabe

2024

International Dairy Journal

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Association mapping of sponge cake volume in U.S. Pacific Northwest elite soft white wheat (Triticum aestivum L.)

Cited by 4 publications

References 20 publications

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

Genetic architecture of end-use quality traits in soft white winter wheat

Effect of components and heating on rheological properties of custard

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