QTL for seed shattering and threshability in intermediate wheatgrass align closely with well‐studied orthologs from wheat, barley, and rice

Altendorf, Kayla R.; DeHaan, Lee R.; Larson, Steve; Anderson, James A.

doi:10.1002/tpg2.20145

Cited by 12 publications

(11 citation statements)

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“…Shattering was rated on a scale of 0 to 5, where 0 indicated no shattering and 5 indicated more than 12 florets shattering per evaluated spike (DeHaan et al, 2018). From 2016 to 2018, shattering was considered a single trait; however, work by Altendorf (2021b) indicated that floret and brittle rachis shattering should be scored separately, so beginning in 2019 brittle rachis was scored as a separate trait in the IWG population. In addition, many other secondary traits including seeds spike −1 , spikelets spike −1 , florets spike −1 , and FSU were evaluated.…”

Section: Phenotypic Assessmentmentioning

confidence: 99%

Genetic architecture and QTL selection response for Kernza perennial grain domestication traits

et al. 2022

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Key message Analysis of multi-year breeding program data revealed that the genetic architecture of an intermediate wheatgrass population was highly polygenic for both domestication and agronomic traits, supporting the use of genomic selection for new crop domestication. Abstract Perennial grains have the potential to provide food for humans and decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®) is a promising perennial grain candidate that The Land Institute has been breeding since 2003. We evaluated four consecutive breeding cycles of IWG from 2016 to 2020 with each cycle containing approximately 1100 unique genets. Using genotyping-by-sequencing markers, quantitative trait loci (QTL) were mapped for 34 different traits using genome-wide association analysis. Combining data across cycles and years, we found 93 marker-trait associations for 16 different traits, with each association explaining 0.8–5.2% of the observed phenotypic variance. Across the four cycles, only three QTL showed an FST differentiation > 0.15 with two corresponding to a decrease in floret shattering. Additionally, one marker associated with brittle rachis was 216 bp from an ortholog of the btr2 gene. Power analysis and quantitative genetic theory were used to estimate the effective number of QTL, which ranged from a minimum of 33 up to 558 QTL for individual traits. This study suggests that key agronomic and domestication traits are under polygenic control and that molecular methods like genomic selection are needed to accelerate domestication and improvement of this new crop.

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Section: Phenotypic Assessmentmentioning

confidence: 99%

Genetic architecture and QTL selection response for Kernza perennial grain domestication traits

et al. 2022

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“…(2019) also identified QTL for multiple traits on chromosome 5 including stem length, and seed nakednesss (threshing ability). In our previous work in this NAM population, chromosome 5 housed QTL for threshing ability, shattering, and brittle rachis (Altendorf et al., 2021c). On chromosome 9, Larson et al.…”

Section: Discussionmentioning

confidence: 86%

“…As genomic selection becomes increasingly routine in the domestication of IWG (Crain et al., 2020a), additional markers for important component traits will be useful. The IWG NAM population has proven to be an effective resource for identifying new QTL, previously identified QTL, and QTL that align closely with known orthologs from other species (Altendorf et al., 2021a, 2021c). Here we applied the IWG NAM population to the analysis of a series of 11 component traits with varying direct and indirect effects on yield (Altendorf et al., 2021b).…”

Section: Discussionmentioning

confidence: 99%

“…The fact that the phenotypic variation among the progeny within a family was only predicted by the variation between parents in very few cases suggests that selecting parents on phenotype alone may not always yield predictable results. For mapping purposes in an outcrossing species like IWG, it is more important that the parents are heterozygous and segregate for the traits of interest (Altendorf et al., 2021a, 2021c).…”

Section: Discussionmentioning

confidence: 99%

“…We previously described a 1,168‐individual, F 1 NAM population of IWG that was developed from 11 phenotypically divergent parents from Cycle 2 of the University of Minnesota breeding program (Altendorf et al, 2021a; Yu et al., 2008). This population has proven effective in the genetic dissection of flowering‐time traits (Altendorf et al., 2021a) and domestication traits, specifically shattering and threshability (Altendorf et al., 2021c). The NAM population was phenotyped for a series of yield‐component traits, which we previously described within the context of environmental effects and the interrelatedness of the traits through structural equation modeling (Altendorf et al., 2021b).…”

Section: Introductionmentioning

confidence: 99%

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Genetic architecture of yield‐component traits in the new perennial grain crop, intermediate wheatgrass

2022

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Intermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth & D.R. Dewey] (IWG) is a perennial, cool‐season grass species currently undergoing direct domestication as one of the first perennial grain crops. To domesticate and improve this obligately outcrossing allohexaploid (2n = 6x = 42), breeders are using both phenotypic‐ and genomic‐assisted recurrent selection methodologies. Thus far, efforts have focused primarily on improving domestication traits and yield, but breeders are limited by the relatively narrow understanding of the genetic control of these traits. An IWG nested association mapping (NAM) population with 1,168 F1 progeny from 10 families was grown in four unique growing environments (St. Paul, MN, and Salina, KS, in 2017 and 2018) and evaluated for a series of 11 yield‐component traits. Using a population‐specific genetic map and 8,003 single‐nucleotide polymorphism (SNP) markers, we used both linkage mapping (LM) and genome‐wide association study (GWAS) to dissect the genetic control of a series of yield‐component traits. We identified 20 significant markers in GWAS and 28 in LM that were detected in at least two environments, several of which were shared across traits. The QTL regions on chromosomes 5 and 9 were significant for eight of 11 traits, and many were detected across multiple analysis methods. The results described herein provide additional resources for incorporating QTL as fixed effects in routine genomic selection pipelines to expedite the gains from selection for yield in this new perennial grain crop.

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Breeding Intermediate Wheatgrass for Grain Production

Bajgain¹,

Crain²,

Cattani³

et al. 2022

Plant Breeding Reviews

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QTL for seed shattering and threshability in intermediate wheatgrass align closely with well‐studied orthologs from wheat, barley, and rice

Abstract: Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

Cited by 12 publications

References 61 publications

Genetic architecture and QTL selection response for Kernza perennial grain domestication traits

Genetic architecture and QTL selection response for Kernza perennial grain domestication traits

Genetic architecture of yield‐component traits in the new perennial grain crop, intermediate wheatgrass

Breeding Intermediate Wheatgrass for Grain Production

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