Genome-Wide Approach to Identify Quantitative Trait Loci for Drought Tolerance in Tetraploid Potato (Solanum tuberosum L.)

Schumacher, Christina; Thümecke, Susanne; Schilling, Florian; Köhl, Karin; Kopka, Joachim; Sprenger, Heike; Hincha, Dirk K.; Walther, Dirk; Seddig, Sylvia; Peters, R J; Zuther, Ellen; Haas, Manuela; Horn, Renate

doi:10.3390/ijms22116123

Cited by 12 publications

(11 citation statements)

References 104 publications

(177 reference statements)

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“…QTL detection of hollow heart is affected by the environment [ 27 ] and genetic background [ 27 , 62 ], since both have effects on the expression of a trait which is the result of the genes responsible. Potential candidate genes in the vicinity of SNP peaks for hollow heart associated with heat and drought stress in potatoes include, Ubiquitin-protein ligase [ 52 , 63 ], Laccase [ 64 ], BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase [ 65 ], Mads box protein [ 63 ], and Zinc finger protein [ 63 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones

Gautam,

Pandey,

Scheuring

et al. 2024

Plants

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Heat stress during the potato growing season reduces tuber marketable yield and quality. Tuber quality deterioration includes external (heat sprouts, chained tubers, knobs) and internal (vascular discoloration, hollow heart, internal heat necrosis) tuber defects, as well as a reduction in their specific gravity and increases in reducing sugars that result in suboptimal (darker) processed products (french fries and chips). Successfully cultivating potatoes under heat-stress conditions requires planting heat-tolerant varieties that can produce high yields of marketable tubers, few external and internal tuber defects, high specific gravity, and low reducing sugars (in the case of processing potatoes). Heat tolerance is a complex trait, and understanding its genetic basis will aid in developing heat-tolerant potato varieties. A panel of 217 diverse potato clones was evaluated for yield and quality attributes in Dalhart (2019 and 2020) and Springlake (2020 and 2021), Texas, and genotyped with the Infinium 22 K V3 Potato Array. A genome-wide association study was performed to identify genomic regions associated with heat-tolerance traits using the GWASpoly package. Quantitative trait loci were identified on chromosomes 1, 3, 4, 6, 8, and 11 for external defects and on chromosomes 1, 2, 3, 10, and 11 for internal defects. Yield-related quantitative trait loci were detected on chromosomes 1, 6, and 10 pertaining to the average tuber weight and tuber number per plant. Genomic-estimated breeding values were calculated using the StageWise package. Clones with low genomic-estimated breeding values for tuber defects were identified as donors of good traits to improve heat tolerance. The identified genomic regions associated with heat-tolerance attributes and the genomic-estimated breeding values will be helpful to develop new potato cultivars with enhanced heat tolerance in potatoes.

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Section: Discussionmentioning

confidence: 99%

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones

Gautam,

Pandey,

Scheuring

et al. 2024

Plants

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“…The data reported here are significant because they derive from a unique and unprecedented mutagenized diploid germplasm panel. All previous mapping studies for the drought-tolerance trait have focused on bi-parental populations ( Anithakumari et al, 2012 ; Khan et al, 2015 ; Schumacher et al, 2021 ); to our knowledge, no previous investigations have reported GWAS mapping for maturity and drought traits in diploid potatoes. Moreover, in the context of changing climate, the identification and development of early-maturity potatoes and potatoes that are drought tolerant are sought as a climate adaptation solution for short- and long-season growing areas.…”

Section: Discussionmentioning

confidence: 99%

“…Most of the genes were identified in a close vicinity (0.5–1 kb) of the QTNs, suggesting their true impact on the traits. In their study using an indirect yield trait (DRYM) for drought tolerance in tetraploid potatoes, Schumacher et al (2021) reported candidate genes for drought tolerance, albeit from very large (1.3 Mb–36.76 Mb) genomic regions. Our data are, thus, highly relevant for targeted gene studies and marker development when compared with the report by Schumacher et al (2021) .…”

Section: Discussionmentioning

confidence: 99%

“…While, drought resistance genes have been reported in other crops ( Shinozaki and Yamaguchi, 2007 ; Joshi et al, 2016 ; Soto-Cerda et al, 2020 ), to our knowledge, only very few studies have been reported on mapping genes conferring drought tolerance in potatoes ( Anithakumari et al, 2012 ; Khan et al, 2015 ; Schumacher et al, 2021 ), all focused on bi-parental populations. Of the previous studies, only Schumacher et al (2021) performed in controlled and field settings and, using an indirect yield trait (the deviation of the relative starch yield median—DRYM) in cultivated tetraploid potato, identified candidate genes located in very large (1.3 Mb–36.76 Mb) genomic regions associated with the DRYM drought-tolerance trait. To date, no candidate genes associated with drought tolerance or maturity, two key traits for potato crop adaptation to changing climate, have been identified in diploid potatoes.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes

Fofana,

Soto-Cerda,

Zaidi

et al. 2024

Front. Genet.

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Cultivated potato (Solanum tuberosum) is known to be highly susceptible to drought. With climate change and its frequent episodes of drought, potato growers will face increased challenges to achieving their yield goals. Currently, a high proportion of untapped potato germplasm remains within the diploid potato relatives, and the genetic architecture of the drought tolerance and maturity traits of diploid potatoes is still unknown. As such, a panel of 384 ethyl methanesulfonate-mutagenized diploid potato clones were evaluated for drought tolerance and plant maturity under field conditions. Genome-wide association studies (GWAS) were conducted to dissect the genetic architecture of the traits. The results obtained from the genetic structure analysis of the panel showed five main groups and seven subgroups. Using the Genome Association and Prediction Integrated Tool–mixed linear model GWAS statistical model, 34 and 17 significant quantitative trait nucleotides (QTNs) were found associated with maturity and drought traits, respectively. Chromosome 5 carried most of the QTNs, some of which were also detected by using the restricted two-stage multi-locus multi-allele-GWAS haploblock-based model, and two QTNs were found to be pleiotropic for both maturity and drought traits. Using the non-parametric U-test, one and three QTNs, with 5.13%–7.4% phenotypic variations explained, showed favorable allelic effects that increase the maturity and drought trait values. The quantitaive trait loci (QTLs)/QTNs associated with maturity and drought trait were found co-located in narrow (0.5–1 kb) genomic regions with 56 candidate genes playing roles in plant development and senescence and in abiotic stress responses. A total of 127 potato clones were found to be late maturing and tolerant to drought, while nine were early to moderate–late maturing and tolerant to drought. Taken together, the data show that the studied germplasm panel and the identified candidate genes are prime genetic resources for breeders and biologists in conventional breeding and targeted gene editing as climate adaptation tools.

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“…Most plants depend on the root system to supply the water and minerals essential for the growth and maintenance of the aboveground organs. A balance is established between the development of the branches and leaves and the development of the root system [ 31 , 32 ]. The development of the root system is much greater than that of the aboveground parts, and the total area of the root system in contact with the soil often exceeds the area of the stem and leaves by a factor of 6–16 [ 33 ].…”

Section: Current Status Of Research On Genes Associated With Root Gro...mentioning

confidence: 99%

Root-Related Genes in Crops and Their Application under Drought Stress Resistance—A Review

Qin

Ali²,

Wang

et al. 2022

IJMS

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Crop growth and development are frequently affected by biotic and abiotic stresses. The adaptation of crops to stress is mostly achieved by regulating specific genes. The root system is the primary organ for nutrient and water uptake, and has an important role in drought stress response. The improvement of stress tolerance to increase crop yield potential and yield stability is a traditional goal of breeders in cultivar development using integrated breeding methods. An improved understanding of genes that control root development will enable the formulation of strategies to incorporate stress-tolerant genes into breeding for complex agronomic traits and provide opportunities for developing stress-tolerant germplasm. We screened the genes associated with root growth and development from diverse plants including Arabidopsis, rice, maize, pepper and tomato. This paper provides a theoretical basis for the application of root-related genes in molecular breeding to achieve crop drought tolerance by the improvement of root architecture.

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Genome-Wide Approach to Identify Quantitative Trait Loci for Drought Tolerance in Tetraploid Potato (Solanum tuberosum L.)

Cited by 12 publications

References 104 publications

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones

Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes

Root-Related Genes in Crops and Their Application under Drought Stress Resistance—A Review

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