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

Improving genomic prediction of vitamin C content in spinach using GWAS-derived markers

Vitamin C (VC), also known as ascorbic acid and ascorbate, is a water-soluble antioxidant in plants that promotes skin health and immune function in humans. Spinach (Spinacia oleracea L.) is a leafy green widely consumed for its health benefits. Recent reports have shown that nutritional content, including VC, can be improved in spinach. However, due to its complex inheritance, new selection methods are needed to improve selection for cultivar development. In this study, single nucleotide polymorphism (SNP) markers identified by genome-wide association (GWAS) were used for genomic prediction (GP) to improve prediction accuracy (PA) for VC content in spinach. A set of 147,977 SNPs generated from whole genome resequencing was used for GWAS in a panel of 347 spinach genotypes by six GWAS models. Sixty-two SNP markers distributed on all six spinach chromosomes were associated with VC content. PA for the selection of VC content was estimated with fourteen random SNP sets across seven GP models. The results indicated that the PA can be > 40% after using 1,000 or more SNPs in six of the seven models tested; using GWAS-derived significant SNP markers PA increases to a high r-value up to 0.7 when using 62 associated SNP markers in Bayes ridge regression (BRR) model. Upon validation, identified accessions with high VC and high PA genomic selection model can be used in spinach breeding programs to develop high VC content cultivars.

Identification of heat stress-related genomic regions by genome-wide association study in Solanum tuberosum

The climate crisis impairs yield and quality of crucial crops like potatoes. We investigated the effects of heat stress on five morpho-physiological parameters in a diverse panel of 178 potato cultivars under glasshouse conditions. Overall, heat stress increased shoot elongation and green fresh weight, but reduced tuber yield, starch content and harvest index. Genomic information was obtained from 258 tetraploid and three diploid cultivars by a genotyping-by-sequencing approach using methylation-sensitive restriction enzymes. This resulted in an enrichment of sequences in gene-rich regions. Population structure analyses using genetic distances and hierarchical clustering revealed strong kinship but weak overall population structure cultivars. A genome-wide association study (GWAS) was conducted with a subset of 20 K stringently filtered SNPs to identify quantitative trait loci (QTL) linked to heat tolerance. We identified 67 QTL and established haploblock boundaries to narrow down the number of candidate genes. Additionally, GO-enrichment analyses provided insights into gene functions. Heritability and genomic prediction were conducted to assess the usability of the collected data for selecting breeding material. The detected QTL might be exploited in marker-assisted selection to develop heat-resilient potato cultivars.

Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance

Climate changes leading to increasingly longer seasonal drought periods in large parts of the world increase the necessity for breeding drought-tolerant crops. Cultivated potato (Solanum tuberosum), the third most important vegetable crop worldwide, is regarded as drought-sensitive due to its shallow root architecture. Two German tetraploid potato cultivars differing in drought tolerance and their F1-progeny were evaluated under various drought scenarios. Bulked segregant analyses were combined with whole-genome sequencing (BSA-Seq) using contrasting bulks of drought-tolerant and drought-sensitive F1-clones. Applying QTLseqr, 15 QTLs comprising 588,983 single nucleotide polymorphisms (SNPs) in 2325 genes associated with drought stress tolerance were identified. SeqSNP analyses in an association panel of 34 mostly starch potato varieties using 1-8 SNPs for each of 188 selected genes narrowed the number of candidate genes down to 10. In addition, ent-kaurene synthase B was the only gene present under QTL 10. Eight of the identified genes (StABP1, StBRI1, StKS, StLEA, StPKSP1, StPKSP2, StYAB5, and StZOG1) address plant development, the other three genes (StFATA, StHGD and StSYP) contribute to plant protection under drought stress. Allelic variation in these genes might be explored in future breeding for drought-tolerant potato varieties.

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

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.

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

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.

Data-driven approaches to improve water-use efficiency and drought resistance in crop plants

With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.

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

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.