Genomic selection for winter survival ability among a diverse collection of facultative and winter wheat genotypes

Beil, Craig T.; Anderson, Victoria A.; Morgounov, Alexey; Haley, Scott D.

doi:10.1007/s11032-018-0925-8

Cited by 10 publications

(8 citation statements)

References 69 publications

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“…Despite the existing variation for winter hardiness and frost tolerance in wheat (Fowler et al, 1977; Longin et al, 2013; Sthapit Kandel et al, 2018), the improvement for these traits has been rather limited, and efforts to enhance them by using exotic sources with excellent winter hardiness like rye have been less promising (Limin and Fowler, 1991). One major reason for this limited genetic progress can be seen in the difficult phenotyping and lack of information concerning winter hardiness when conducting selection decisions caused by the absence or irregular occurrences of winter damage in field trials (Beil et al, 2019) that are in some years replaced by complete winter kill of an entire plant stand (Fowler, 1979).…”

Section: Introductionmentioning

confidence: 99%

“…Hence, numerous studies have been conducted to dissect the genetic architecture of winter hardiness and frost tolerance that revealed the importance of the homologous loci Vrn-A1 , Vrn-B1 , and Vrn-D1 located on the chromosome 5 group both for vernalization response and frost tolerance in wheat (Koemel et al, 2004), with the latter two loci being though fixed for the winter type allele at least in European winter wheat (Langer et al, 2014), although they can be interesting for breeding facultative wheat varieties (Beil et al, 2019). The copy number variation of Vrn-A1 has, on the other hand, been shown to influence both the vernalization response as well as frost tolerance of winter wheat (Díaz et al, 2012; Zhu et al, 2014; Würschum et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection

Michel

Löschenberger²,

Hellinger

et al. 2019

Front. Plant Sci.

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Winter hardiness is a major constraint for autumn sown crops in temperate regions, and thus an important breeding goal in the development of new winter wheat varieties. Winter hardiness is though influenced by many environmental factors rendering phenotypic selection under field conditions a difficult task due to irregular occurrence or absence of winter damage in field trials. Controlled frost tolerance tests in growth chamber experiments are, on the other hand, even with few genotypes, often costly and laborious, which makes a genomic breeding strategy for early generation selection an attractive alternative. The aims of this study were thus to compare the merit of marker-assisted selection using the major frost tolerance QTL Fr-A2 with genomic prediction for winter hardiness and frost tolerance, and to assess the potential of combining both measures with a genomic selection index using a high density marker map or a reduced set of pre-selected markers. Cross-validation within two training populations phenotyped for frost tolerance and winter hardiness underpinned the importance of Fr-A2 for frost tolerance especially when upweighting its effect in genomic prediction models, while a combined genomic selection index increased the prediction accuracy for an independent validation population in comparison to training with winter hardiness data alone. The prediction accuracy could moreover be maintained with pre-selected marker sets, which is highly relevant when employing cost reducing fingerprinting techniques such as targeted genotyping-by-sequencing. Genomic selection showed thus large potential to improve or maintain the performance of winter wheat for these difficult, costly, and laborious to phenotype traits.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection

Michel

Löschenberger²,

Hellinger

et al. 2019

Front. Plant Sci.

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“…Genotyping crossing parents as in the mid-parent method has moreover several conceptional advantages in comparison with the pedigree method, e.g., the option to genomically plan crosses for a more efficient diversity management within a breeding program (Osthushenrich et al 2017 ; Akdemir et al 2019 ; Neyhart et al 2019 ). Further possibilities opened up by genotyping crossing parents are the availability of genomic predictions for difficult to phenotype traits that cannot be observed every year, like winter hardiness (Beil et al 2019 ; Michel et al 2019 ), or for costly to phenotype traits like baking quality (Hayes et al 2017 ; Ben-Sadoun et al 2020 ) and mycotoxin content (Haikka et al 2020b ; Verges et al 2020 ). These predictions can be valuable inputs to further guide parental choices as phenotyping for these traits might be restricted to a few best performing advanced generation lines in small-scale breeding programs.…”

Section: Discussionmentioning

confidence: 99%

Genotyping crossing parents and family bulks can facilitate cost-efficient genomic prediction strategies in small-scale line breeding programs

Michel

Löschenberger²,

Ametz³

et al. 2021

Theor Appl Genet

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Key message Genomic relationship matrices based on mid-parent and family bulk genotypes represent cost-efficient alternatives to full genomic prediction approaches with individually genotyped early generation selection candidates. Abstract The routine usage of genomic selection for improving line varieties has gained an increasing popularity in recent years. Harnessing the benefits of this approach can, however, be too costly for many small-scale breeding programs, as in most genomic breeding strategies several hundred or even thousands of lines have to be genotyped each year. The aim of this study was thus to compare a full genomic prediction strategy using individually genotyped selection candidates with genomic predictions based on genotypes obtained from pooled DNA of progeny families as well as genotypes inferred from crossing parents. A population of 722 wheat lines representing 63 families tested in more than 100 multi-environment trials during 2010–2019 was for this purpose employed to conduct an empirical study, which was supplemented by a simulation with genotypic data from further 3855 lines. A similar or higher prediction ability was achieved for grain yield, protein yield, and the protein content when using mid-parent or family bulk genotypes in comparison with pedigree selection in the empirical across family prediction scenario. The difference of these methods with a full genomic prediction strategy became furthermore marginal if pre-existing phenotypic data of the selection candidates was already available. Similar observations were made in the simulation, where the usage of individually genotyped lines or family bulks was generally preferable with smaller family sizes. The proposed methods can thus be regarded as alternatives to full genomic or pedigree selection strategies, especially when pedigree information is limited like in the exchange of germplasm between breeding programs.

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“…Further, the multiple QTL for FT and WH [19] with low to moderate R 2 indicated that genomic selection (GS) could be a viable option to improve these traits. GS is becoming an effective method for the rapid selection of superior genotypes for cold hardiness improvement in different crops [28,29]. Therefore, we also suggest using GS in alfalfa to capture maximum genetic variability present in the germplasms.…”

Section: Ft Qtl and Potential Applicationmentioning

confidence: 99%

Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping

Adhikari¹,

Makaju²,

Lindstrom³

et al. 2020

Preprint

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Background Winter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were phenotyped for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping by sequencing (GBS) and the QTL associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild. Results Alfalfa FT screening method optimized in this experiment comprises three major steps; clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is useful as an indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL for four traits; visual rating-based FT, percentage survival (PS), treated to control regrowth ratio (RR), and treated to control biomass ratio (BR). Some QTL overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) potentially represented the genic region of a cold tolerance gene, the c-repeat binding factor (CBF). These QTL were located on the terminal end of chromosome 6 which is considered a location of the CBF homologs in alfalfa.Conclusions The indoor freezing tolerance selection method reported here is valuable for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources needed by the alfalfa research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement.

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Genomic selection for winter survival ability among a diverse collection of facultative and winter wheat genotypes

Cited by 10 publications

References 69 publications

Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection

Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection

Genotyping crossing parents and family bulks can facilitate cost-efficient genomic prediction strategies in small-scale line breeding programs

Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping

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