Prediction based on estimated breeding values using genealogy for tuber yield and late blight resistance in auto-tetraploid potato (Solanum tuberosum L.)

Sood, Salej; Bhardwaj, Vinay; Kaushik, S. K.; Sharma, Sanjeev

doi:10.1016/j.heliyon.2020.e05624

Cited by 11 publications

(15 citation statements)

References 23 publications

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“…In comparison to study of Zhang et al 4; Supplementary Table 3) could be targeted for verification and use for practical plant breeding. The numerous genomic regions/SNPs suggest that leaf spot diseases are regulated by multiple loci with both minor and major effects, hence selection based on only phenotypic data may be misleading (Sood et al, 2020). In addition to the above, a number of SNPs that colocalized with multiple indices assessed in this study could be useful in developing models that could distinguish between ELS and LLS.…”

Section: Discussionmentioning

confidence: 90%

“…Hence, AX-176801892 (Chr02, LOD= 3.18-3.99; PVE= 0.05-3.49%) linked to ELS, AX-176799357 (Chr04, LOD= 7.73-16.45; PVE= 12.78-20.69%) linked to LLS, AX-176806210 (Chr04, LOD=3.20-9.84; PVE=7.21-38.50%) linked to AUDPC-LLS, AX-147224496 (Chr04, LOD= 4.36-5.46; PVE= 0.01-10.15%) linked to NDVI and several others ( Table 4 ; Supplementary Table 3 ) could be targeted for verification and use for practical plant breeding. The numerous genomic regions/SNPs suggest that leaf spot diseases are regulated by multiple loci with both minor and major effects, hence selection based on only phenotypic data may be misleading ( Sood et al., 2020 ). In addition to the above, a number of SNPs that colocalized with multiple indices assessed in this study could be useful in developing models that could distinguish between ELS and LLS.…”

Section: Discussionmentioning

confidence: 99%

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Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

Oteng‐Frimpong

Karikari²,

Sie³

et al. 2023

Front. Plant Sci.

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Early leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in ≤ 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at ± 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.

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Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

Oteng‐Frimpong

Karikari²,

Sie³

et al. 2023

Front. Plant Sci.

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“…A linear mixed model, pedigree BLUP was fitted for each trait separately to estimate the BLUP breeding values (EBVs) as described earlier by Slater et al (2014) and Sood et al (2020b).…”

Section: Methodsmentioning

confidence: 99%

“…Year and environment information can be fitted as fixed effects in the BLUP model (Piepho et al 2008). There are very few reports of use of BLUP breeding values for prediction of genetic merit of breeding lines in potato breeding (Slater et al 2014;Slater et al 2016;Endelman et al 2018;Sood et al 2020a;Sood et al 2020b). Thus, the study was carried out to assess the feasibility of BLUP breeding values based selection of parental lines in potato breeding in India for the first time.…”

Section: Introductionmentioning

confidence: 99%

Identification of superior parental lines based on BLUP breeding values in potato (Solanum tuberosum L.)

Sood¹,

Bhardwaj²,

Kaushik³

et al. 2022

IJGPB

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Identification of superior parental lines require phenotypic or genotypic characterization of the germplasm, which is time consuming and laborious. The advanced potato breeding clones including control varieties were evaluated under field conditions to identify the suitable parental lines for tuber yield, late blight and specific gravity based on estimated breeding values using historical data as training population during 2008-09 to 2019-20. Pedigree of all the clones was searched to a depth of 5-6 generations. The mixed model fitting using REML was true. The minimum and maximum values for total tuber yield, late blight area under disease progress curve (AUDPC) and specific gravity were 28.33-732.2, 0-1846.25, 1.043-1.087, respectively. Pedigree had 161 founders out of total 759 individuals and the pedigree matrix showed relationship in 1,09,057 pairs. Heritability estimate was highest for specific gravity (0.77) followed by late blight AUDPC (0.49) and total tuber yield (0.24). The estimate of the BLUP breeding values (EBVs) for total tuber yield were highest for Kufri Mohan, Kufri Pukhraj, Kufri Khyati, SM/14-342 and Kufri Pushkar while SM/10-05, SM/09-99, Kufri Girdhari, SM/11-120 and Kufri Karan for late blight resistance, and Kufri Chipsona-1, SM/14-225, SM/14-229, SM/10-220 and SM/09-153 for specific gravity were the best genotypes. The prediction accuracy measured as correlation between EBV and observed phenotype score for specific gravity (0.97) was near perfect, very high for late blight AUDPC (0.75), and high for total tuber yield (0.55). The prediction bias measured as regression coefficient and scatter plots of observed phenotype values on EBVs was nil to low for specific gravity andlate blight AUDPC, while underestimation was observed for total tuber yield. Overall, the prediction accuracies for all the three traits were very good and selection of parental lines using Best Linear Unbiased Prediction breeding values could result in enhanced genetic gain in potato breeding

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“…As demonstrated in the modern tetraploid potato crop, information about pedigree is essential to achieving suitable association mapping [8,9], for deciphering genome-wide conserved patterns in elite potato parental lines [10], and for studies on the inheritance of extreme resistance [11]. The use of genealogical information is also helpful in estimating breeding values and improving genetic gains for low heritability traits in potato breeding [12,13]. Although many studies have attempted to identify the origins of the cultivated potato in Europe [14][15][16][17][18][19][20], and how much it has diversified [6,21], many questions remain.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview

Spanoghe

Marique

Nirsha

et al. 2022

Biology

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We investigated the changes in genetic diversity over time and space of the cultivated potato (Solanum tuberosum L.) for the period pre-1800 to 2021. A substantial panel of 1219 potato varieties, belonging to different spatiotemporal groups, was examined using a set of 35 microsatellite markers (SSR). Genotypic data covering a total of 407 alleles was analyzed using both self-organizing map (SOM) and discriminant analysis of principal components (DAPC) de novo and a priori clustering methods, respectively. Data analysis based on different models of genetic structuring provided evidence of (1) at least two early lineages that have been maintained since their initial introduction from the Andes into Europe in the 16th century, followed by later ones coming from reintroduction events from the US in the mid-1800s; (2) a level of diversity that has gradually evolved throughout the studied time periods and areas, with the most modern variety groups encompassing most of the diversity found in earlier decades; (3) the emergence of new genetic groups within the current population due to increases in the use of germplasm enhancement practices using exotic germplasms. In addition, analysis revealed significant genetic differentiation both among and within the spatiotemporal groups of germplasm studied. Our results therefore highlight that no major genetic narrowing events have occurred within the cultivated potato over the past three centuries. On the contrary, the genetic base shows promising signs of improvement, thanks to extensive breeding work that is gaining momentum. This overview could be drawn on not only to understand better how past decisions have impacted the current genetic cultivated potato resources, but also to develop appropriate new strategies for breeding programs consistent with the socio-economic and sustainability challenges faced by agrifood systems.

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Prediction based on estimated breeding values using genealogy for tuber yield and late blight resistance in auto-tetraploid potato (Solanum tuberosum L.)

Cited by 11 publications

References 23 publications

Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

Identification of superior parental lines based on BLUP breeding values in potato (Solanum tuberosum L.)

Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview

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