Genomic Prediction in a Multiploid Crop: Genotype by Environment Interaction and Allele Dosage Effects on Predictive Ability in Banana

Nyine, Moses; Uwimana, Brigitte; Blavet, Nicolas; Hřibová, Eva; Vanrespaille, Helena; Batte, Michael; Akech, Violet; Brown, Allan; Lorenzen, J.; Swennen, Rony; Doležel, Jaroslav

doi:10.3835/plantgenome2017.10.0090

Cited by 47 publications

(54 citation statements)

References 67 publications

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“…The imputed D-genome SNPs were split into subsets based on families. A 195 combination of custom Perl and R scripts (Nyine et al 2018), were used to convert the SNP 196 alleles to 0, 1, and 2, of which, 0 is homozygous major allele, 1 is heterozygous and 2 is 197 homozygous minor allele. Regions containing monomorphic SNPs were eliminated by the R 198 script.…”

Section: Recombination Hotspots 194mentioning

confidence: 99%

Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

Nyine

Adhikari

Clinesmith

et al. 2019

Preprint

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16Wild relatives of hexaploid wheat (Triticum aestivum) are the reservoirs of novel allelic 17 diversity with great potential to improve many agronomic traits in wheat. Here, we 18 investigated the genome-wide patterns and efficiency of Aegilops tauschii allele introgression 19 into the winter wheat cultivars. The introgression population of 351 BC 1 F 3 : 5 lines was 20 selected based on phenology and development characteristics from crosses between six 21 hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. Complexity reduced genomic 22 library sequencing was used to develop SNP markers and infer the regions of identity-by-23 descent and the boundaries of the introgressed segments. Using a diverse panel of 116 Ae. 24 tauschii accessions, it was possible to infer that introgression lines had single or multiple IBD 25 segments from accessions of diverse geographic origin. Introgression frequency was high at 26 the ends of chromosomes and low in the large pericentromeric 2/3 of the chromosome arms 27 characterized by low crossover rate. While the effect of selection for free-threshing genotypes 28 was evident around the domestication gene Tg, reduction in the frequency of introgression 29 was limited to relatively small regions flanking the gene. These results suggest that the 30 effects of phenotypic selection on the introgressed wild relative's alleles at the early 31 generations of population development are strongly influenced by the distribution of 32 crossover frequency across genome, consistent with the Hill-Robertson effect. Our study 33 offers insights into the introgression population development to ensure retention of genetic 34 2 diversity across entire genome and presents a resource that will be valuable for deploying 35 wild relative diversity in breeding programs to create climate resilient and disease resistant 36 varieties with improved yield and quality traits. 37 38Introduction 39Wheat production is constrained by several biotic and abiotic factors, yet the demand 40 for wheat is expected to double by 2050. A yield increase of ~2.4 % per year has been 41 projected as required to close the gap between the current production level and an increasing 42 demand (Ray et al. 2013). While this goal can be achieved by improving agronomic 43 practices, expanding the production area and/or deployment of high-yielding wheat varieties, 44 the first two alternatives are unsustainable because land is a limited resource and most 45 effective agronomic practices are costly. Accelerated wheat improvement through extensive 46 deployment of available genomics tools and genetic resources, including close and distant 47 wild relatives of wheat, is viewed as the most effective and sustainable alternative to 48 increasing yield. 49Allohexaploid wheat, Triticum aestivum (2n = 6x = 42, AABBDD) resulted from 50 hybridization of Triticum turgidum (2n = 4x = 28, AABB) and Aegilops tauschii ssp. 51 strangulata (2n = 2x = 14, DD) (Kihara 1944; Luo et al. 2007;Wang et al. 2013). 52 Domestication of wheat followed by con...

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Section: Recombination Hotspots 194mentioning

confidence: 99%

Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

Nyine

Adhikari

Clinesmith

et al. 2019

Preprint

Self Cite

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“…SNP calling (Slater et al, 2016;Gezan et al, 2017;Bourke et al, 2018). A few studies have demonstrated the potential advantages of GS in allo and autopolyploids (Gezan et al, 2017;Enciso-Rodriguez et al, 2018;Nyine et al, 2018;Amadeu et al, 2019;de Bem Oliveira et al, 2019;Juliana et al, 2019;Zingaretti et al, 2019), although its implementation is still in its infancy.…”

Section: Introductionmentioning

confidence: 99%

Exploring Deep Learning for Complex Trait Genomic Prediction in Polyploid Outcrossing Species

et al. 2020

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“…; Slater et al , 2016; Sverrisdottir el al. 2017; Nyine et al 2018; Endelman et al 2018). It is interesting to note that genotype classification is one of the major challenges for polyploids.…”

Section: Introductionmentioning

confidence: 99%

Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in the phenotype prediction

Oliveira

Resende

Ferrao

et al. 2018

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27Estimation of allele dosage in autopolyploids is challenging and current methods 28 often result in the misclassification of genotypes. Here we propose and compare the use of 29 next generation sequencing read depth as continuous parameterization for autotetraploid 30 genomic prediction of breeding values, using blueberry (Vaccinium corybosum spp.) as a 31 model. Additionally, we investigated the influence of different sources of information to 32 build relationship matrices in phenotype prediction; no relationship, pedigree, and genomic 33 information, considering either diploid or tetraploid parameterizations. A real breeding 34 population composed of 1,847 individuals was phenotyped for eight yield and fruit quality 35 traits over two years. Analyses were based on extensive pedigree (since 1908) and high-36 density marker data (86K markers). Our results show that marker-based matrices can yield 37 significantly better prediction than pedigree for most of the traits, based on model fitting and 38 expected genetic gain. Continuous genotypic based models performed as well as the current 39 best models and presented a significantly better goodness-of-fit for all traits analyzed. This 40 approach also reduces the computational time required for marker calling and avoids 41 problems associated with misclassification of genotypic classes when assigning dosage in 42 polyploid species. Accuracies are encouraging for application of genomic selection (GS) for 43 blueberry breeding. Conservatively, GS could reduce the time for cultivar release by three 44 years. GS could increase the genetic gain per cycle by 86% on average when compared to 45 phenotypic selection, and 32% when compared with pedigree-based selection.46 47 48 Polyploidy events are not an exception in plants, as about 70% of Angiosperms and 53 95% of Pteridophytes underwent at least one polyploidization event (Soltis and Soltis 1999). 54 Polyploids are normally grouped into two categories, autopolyploids and allopolyploids, but 55 intermediate forms are also possible, such as segmental allopolyploids (Spoelhof et al. 2017). 56 Thresholds for polyploid classification have been controversial, but following the general 57 taxonomic definition, autopolyploids arise from within-species whole genome duplication, 58 and allopolyploids arise from whole genome duplication prior to or after an inter-specific 59 hybridization event (Soltis et al. 2007). 60 Because speciation via ploidy increase can generate new phenotypic variability, this 61 phenomenon is considered a powerful evolutionary source (Hieter and Griffiths 1999; Soltis 62 et al. 2016). Despite the important role of polyploidization in plant evolution, its effects on 63 inheritance of many agronomic traits and population genetics are still poorly understood 64 when compared with diploid species (Dufresne et al. 2014). This especially holds true for 65 autopolyploids. The complex nature of autopolyploid genetics is due to the presence of 66 genotypes with higher allele dosage than diploids, larger number ...

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Genomic Prediction in a Multiploid Crop: Genotype by Environment Interaction and Allele Dosage Effects on Predictive Ability in Banana

Cited by 47 publications

References 67 publications

Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

Exploring Deep Learning for Complex Trait Genomic Prediction in Polyploid Outcrossing Species

Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in the phenotype prediction

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