Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress

Abstract

BackgroundImprovement of water-use efficiency (WUE) can effectively reduce production losses caused by drought stress. A better understanding of the genetic determination of WUE in crops under drought stress has great potential value for developing cultivars adapted to arid regions. To identify the genetic loci associated with WUE and reveal genes responsible for the trait in apple, we aim to map the quantitative trait loci (QTLs) for carbon isotope composition, the proxy for WUE, applying two contrasting irrigating regimes over the two-year experiment and search for the candidate genes encompassed in the mapped QTLs.ResultsWe constructed a high-density genetic linkage map with 10,172 markers of apple, using single nucleotide polymorphism (SNP) markers obtained through restriction site-associated DNA sequencing (RADseq) and a final segregating population of 350 seedlings from the cross of Honeycrisp and Qinguan. In total, 33 QTLs were identified for carbon isotope composition in apple under both well-watered and drought-stressed conditions. Three QTLs were stable over 2 years under drought stress on linkage groups LG8, LG15 and LG16, as validated by Kompetitive Allele-Specific PCR (KASP) assays. In those validated QTLs, 258 genes were screened according to their Gene Ontology functional annotations. Among them, 28 genes were identified, which exhibited significant responses to drought stress in ‘Honeycrisp’ and/or ‘Qinguan’. These genes are involved in signaling, photosynthesis, response to stresses, carbohydrate metabolism, protein metabolism and modification, hormone metabolism and transport, transport, respiration, transcriptional regulation, and development regulation. They, especially those for photoprotection and relevant signal transduction, are potential candidate genes connected with WUE regulation in drought-stressed apple.ConclusionsWe detected three stable QTLs for carbon isotope composition in apple under drought stress over 2 years, and validated them by KASP assay. Twenty-eight candidate genes encompassed in these QTLs were identified. These stable genetic loci and series of genes provided here serve as a foundation for further studies on marker-assisted selection of high WUE and regulatory mechanism of WUE in apple exposed to drought conditions, respectively.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1308-3) contains supplementary material, which is available to authorized users.

Dissection of Quantitative Trait Loci (QTL), annotation of Single Nucleotide Polymorphism (SNP), and Identification of Candidate Genes for Grain Yield in Triticum turgidum L. var durum

“…We found among 9 QTLs related to grain yield, four were located on 2A chromosome, these QTLs were detected in diverse stressed environments: EP characterized by cold, INC and RF by drought, and RQ by heat. These results are in accordance with several studies on grain yield QTLs located on 2A chromosome [24,32,33].…”

“…For the QTLs detection in specific and stressed environments, 9 QTLs were detected, 4 of which were localized on 2A, due to its strong contribution to grain yield [32,33], the full DNA sequence of 2A chromosome were downloaded from URGI and the 4 DNA sequences corresponding to the 4 QTL were isolated based on markers flanking of these QTL regions [24,25,29] using the GeneStudio software. More informations about the environments, DNA sequences size, environmental conditions, QTL intervals and flanking markers are summarized in Table 1.…”

Apple whole genome sequences: recent advances and new prospects

“…In another family, three QTLs (on LGs 8, 15, and 16) were identified for carbon isotope discrimination (Δ 13 C), which is a proxy for seasonal WUE. These QTLs were stable across two years in a “Honeycrisp” × “Qinguan” family, and the LG 8 QTL co-localized with one of the previously mentioned QTLs for transpiration rate 133 . The WGS allowed the identification of 28 QTL-associated candidate genes and differentially expressed transcription factors between the high and low WUE cultivars “Qinguan” and “Honeycrisp”, respectively 134 , under drought stress 133 .…”

“…These QTLs were stable across two years in a “Honeycrisp” × “Qinguan” family, and the LG 8 QTL co-localized with one of the previously mentioned QTLs for transpiration rate 133 . The WGS allowed the identification of 28 QTL-associated candidate genes and differentially expressed transcription factors between the high and low WUE cultivars “Qinguan” and “Honeycrisp”, respectively 134 , under drought stress 133 . Zhou and co-workers 135 identified and characterized the MdAGO gene family coding for Argonaute proteins in apple and found them to be induced by drought, salt, cold, and ABA treatment, and MdAGO4.1 was upregulated in the WUE cultivar “Qinguan” during water stress.…”

Integration of QTL, Transcriptome and Polymorphism Studies Reveals Candidate Genes for Water Stress Response in Tomato

“…However, the degree of sensitivity to WD can vary widely between cultivars/genotypes within a species. Genetic determinants of plant responses to WD have been studied in several species and genotype-phenotype associations under WD conditions have yielded many quantitative trait loci (QTLs) affecting plant responses to WD [11][12][13]. Tomato growth and development are affected by WD stress and an extensive genotype × watering regime interaction (G × W) has been observed in different experimental populations for the crop [14][15][16][17][18].…”