Domestication to Twenty-First-Century Potato Cultivars

Bradshaw, J. E.

doi:10.1007/978-3-030-64414-7_1

Cited by 5 publications

(5 citation statements)

References 137 publications

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“…The use of MT and ME models for genomic prediction in this research led to highest accuracy for tuber yield and tuber flesh starch as per available literature. Tuber flesh starch, which is often estimated from specific gravity measurements, is a very highly heritable trait (Bradshaw, 2021, Ortiz et al, 2021) that is affected very little by the genotype × environment interactions (Killick and Simmonds, 1974), thus explaining the high prediction accuracy noted in this and research elsewhere. The high prediction accuracy noted in this, and previous research suggest that developing GEBV modeling in potato for tuber flesh starch does not require a very large training population but just a few hundred (including both breeding clones and released cultivars that are relevant to the breeding program and covering a broad range of trait variation) may suffice.…”

Section: Discussionmentioning

confidence: 86%

Modeling genotype × environment interaction for single- and multi-trait genomic prediction in potato (Solanum tuberosum L.)

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et al. 2022

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In this study we extend research on genomic prediction (GP) to polysomic polyploid plant species with the main objective to investigate single trait (ST) versus multi-trait (MT) for multi-environment (ME) models for the combination of three locations in Sweden (Helgegrden [HEL], Mosslunda [MOS], Ume [UM]) over two year-trials (2020, 2021) of 253 potato cultivars and breeding clones for five tuber weight traits and two tuber flesh quality characteristics. This research investigated the GP of four genome-based prediction models with genotype environment interactions (GE): (1) single trait reaction norm model (M1), (2) single trait model considering covariances between environments (M2), (3) single trait M2 extended to include a random vector that utilizes the environmental covariances (M3) and (4) multi-trait model with GE (M4). Several prediction problems were analyzed for each of the GP accuracy of the four models. Results of the prediction of traits in HEL, the high yield potential testing site in 2021, show that the best predicted traits were tuber flesh starch (%), weight of tuber above 60 or below 40 mm in size, and total tuber weight. In terms of GP, accuracy model M4gave the best prediction accuracy in three traits, namely tuber weight of 4050 or above 60 mm in size, and total tuber weight and very similar in the starch trait. For MOS in 2021, the best predictive traits were starch, weight of tuber above 60, 5060, or below 40 mm in size, and total tuber weight. MT model M4 was the best GP model based on its accuracy when some cultivars are observed in some traits. For GP accuracy of traits in UM in 2021, the best predictive traits were weight of tuber above 60, 5060, or below 40 mm in size and the best model was MT M4 followed by models ST M3 and M2.

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Section: Discussionmentioning

confidence: 86%

Modeling genotype × environment interaction for single- and multi-trait genomic prediction in potato (Solanum tuberosum L.)

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et al. 2022

Preprint

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“…In contrast, Phureja is more genetically homogeneous with fewer accessions ( Ellis et al., 2018 ). As documented by different authors, the genetic diversity of native tetraploid potatoes from the Andigenum group has broader geographic coverage and diversity compared to the Phureja group distributed in a more restricted area ( Hawkes, 1990 ; Huamán and Spooner, 2002 ; Spooner et al., 2010 ; Bradshaw, 2021 ), which suggests that polyploidy gave advantages of yield, robustness, and adaptation to different environments in the Andean Highlands. Although the Phureja diploids are also derived from S. stenotomum , they were selected due to a lack of tuber dormancy, shorter crop cycles, and adaptability to warmer, lower, and eastern valleys of the Andes.…”

Section: Discussionmentioning

confidence: 86%

“…From this ample distribution, several thousand potato landraces have been reported with broad genetic diversity that can be described at various levels: morphological, physiological, and agronomic are just some to be highlighted. Some authors have reported extensive diversity in tuber skin and flesh color, tuber and leaf shape, floral colors, growth habit, maturity, dormancy, and photoperiod length needed for tuberization, in addition to pest and disease resistance, environmental responsiveness, and tuber yield ( Spooner et al., 2010 ; Ellis et al., 2020 ; Bradshaw, 2021 ). This extensive diversity represents a reservoir of genes for crop improvement, food security, and adaptability to climate change (ibid).…”

Section: Introductionmentioning

confidence: 99%

Defining a diverse core collection of the Colombian Central Collection of potatoes: a tool to advance research and breeding

et al. 2023

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The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions ― an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC’s genetic diversity. The analysis of molecular variance confirmed the CCC’s diversity with a significant population structure (Phi=0.359; p-value=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count.

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“…The use of MT and ME models for GP in this research led to the highest accuracy for tuber yield and tuber flesh starch as per available literature. Tuber flesh starch, which is often estimated from specific gravity measurements, is a very highly heritable trait ( Bradshaw 2021 ; Ortiz et al . 2021 ) that is affected very little by the GEs ( Killick and Simmonds 1974 ), thus explaining the high prediction accuracy noted in this and research elsewhere.…”

Section: Discussionmentioning

confidence: 99%

Modeling genotype × environment interaction for single and multitrait genomic prediction in potato (Solanum tuberosum L.)

Cuevas

Reslow

Crossa

et al. 2022

View full text Add to dashboard Cite

In this study we extend research on genomic prediction (GP) to polysomic polyploid plant species with the main objective to investigate single trait (ST) and multi-trait (MT) multi-environment (ME) models using field trial data from three locations in Sweden (Helgegården [HEL], Mosslunda [MOS], Umeå [UM]) over two years (2020, 2021) of 253 potato cultivars and breeding clones for five tuber weight traits and two tuber flesh quality characteristics. This research investigated the GP of four genome-based prediction models with genotype × environment interactions (GE): (1) ST reaction norm model (M1), (2) ST model considering covariances between environments (M2), (3) ST M2 extended to include a random vector that utilizes the environmental covariances (M3) and (4) MT model with GE (M4). Several prediction problems were analyzed for each of the GP accuracy of the four models. Results of the prediction of traits in HEL, the high yield potential testing site in 2021, show that the best predicted traits were tuber flesh starch (%), weight of tuber above 60 or below 40 mm in size, and total tuber weight. In terms of GP, accuracy model M4 gave the best prediction accuracy in three traits, namely tuber weight of 40–50 or above 60 mm in size, and total tuber weight and very similar in the starch trait. For MOS in 2021, the best predictive traits were starch, weight of tuber above 60, 50–60, or below 40 mm in size, and total tuber weight. MT model M4 was the best GP model based on its accuracy when some cultivars are observed in some traits. For GP accuracy of traits in UM in 2021, the best predictive traits were weight of tuber above 60, 50–60, or below 40 mm in size and the best model was MT M4 followed by models ST M3 and M2.

show abstract

Domestication to Twenty-First-Century Potato Cultivars

Cited by 5 publications

References 137 publications

Modeling genotype × environment interaction for single- and multi-trait genomic prediction in potato (Solanum tuberosum L.)

Modeling genotype × environment interaction for single- and multi-trait genomic prediction in potato (Solanum tuberosum L.)

Defining a diverse core collection of the Colombian Central Collection of potatoes: a tool to advance research and breeding

Modeling genotype × environment interaction for single and multitrait genomic prediction in potato (Solanum tuberosum L.)

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