Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance

Lau, Kin H.; Herrera, Mariana; Crisovan, Emily; Wu, Shan; Fei, Zhangjun; Khan, Muhammad Awais; Buell, C. Robin; Gemenet, Dorcus C.

doi:10.1002/pld3.92

Cited by 22 publications

(39 citation statements)

References 72 publications

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“…Remarkably, the DEGs encoded kinases, such as receptor-like kinases and LRR receptor-like kinase, were found to be largely up-regulated after 6, 12, and 48 h of PEG-induced drought stress. It is well established that LRR-RLKs play a valuable role in response to drought stress 82 . On the other hand, a substantial number of DEGs were downregulated under drought stress as compared to the control at different time points.…”

Section: Discussionmentioning

confidence: 99%

RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato

Arisha

Ahmad

Tang

et al. 2020

Sci Rep

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Purple-fleshed sweet potato (PFSP) is an important food crop, as it is a rich source of nutrients and anthocyanin pigments. Drought has become a major threat to sustainable sweetpotato production, resulting in huge yield losses. Therefore, the present study was conducted to identify drought stressresponsive genes using next-generation (NGS) and third-generation sequencing (TGS) techniques. Five cDNA libraries were constructed from seedling leaf segments treated with a 30% solution of polyethylene glycol (PEG-6000) for 0, 1, 6, 12, and 48 h for second-generation sequencing. Leaf samples taken from upper third of sweet potato seedlings after 1, 6, 12, and 48 h of drought stress were used for the construction of cDNA libraries for third-generation sequencing; however, leaf samples from untreated plants were collected as controls. A total of 184,259,679 clean reads were obtained using second and third-generation sequencing and then assembled into 17,508 unigenes with an average length of 1,783 base pairs. Out of 17,508 unigenes, 642 (3.6%) unigenes failed to hit any homologs in any databases, which might be considered novel genes. A total of 2, 920, 1578, and 2,418 up-regulated unigenes and 3,834, 2,131, and 3,337 down-regulated unigenes from 1 h, 6 h, 12 h, and 48 h library were identified, respectively in drought stress versus control. In addition, after 6, 12, and 48 h of drought stress, 540 up-regulated unigenes, 486 down-regulated unigenes and 414 significantly differentially expressed unigenes were detected. It was found that several gene families including Basic Helix-loop-helix (bHLH), basic leucine zipper (bZIP), Cystein2/Histidine2 (C2H2), C3H, Ethylene-responsive transcription factor (ERF), Homo domain-leucine zipper (HD-ZIP), MYB, NAC (NAM, ATAF1/2, and CUC2), Thiol specific antioxidant and WRKY showed responses to drought stress. In total, 17,472 simple sequence repeats and 510,617 single nucleotide polymorphisms were identified based on transcriptome sequencing of the PFSP. About 96.55% of the obtained sequences are not available online in sweet potato genomics resources. Therefore, it will enrich annotated sweet potato gene sequences and enhance understanding of the mechanisms of drought tolerance through genetic manipulation. Moreover, it represents a sequence resource for genetic and genomic studies of sweet potato. Purple-fleshed sweet potato (PFSP) (Ipomoea batatas (L.) Lam.) is a type of sweet potato, which has purple skin and flesh color of the storage roots due to the large accumulation of anthocyanin pigments 1. It is a root crop widely grown in some Asian and African countries (i.e. China, India, and Kenya). Sweet potato is regarded as the seventh most important food crop. It is among the crops which generate large amounts of food per unit area per unit time 2. Furthermore, it is considered to be a cheap source of energy, carbohydrates, vitamin, potassium, iron, fiber, and protein 3 .

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Section: Discussionmentioning

confidence: 99%

RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato

Arisha

Ahmad

Tang

et al. 2020

Sci Rep

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“…Tanzania RNA was isolated, and libraries were constructed and sequenced as described by Wu et al (2018). To assess expression abundances, both Beauregard and Tanzania RNA-sequencing reads were cleaned, aligned to the I. trifida genome, and fragments per kb exon model per million mapped reads (FPKM) were determined as previously described in Lau et al (2018). For the final FPKM matrix, genes encoded by the chloroplast were removed.…”

Section: Gene Expression Profilingmentioning

confidence: 99%

Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]

et al. 2019

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Key message β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated. Abstract In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F 1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security.

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“…trifida genome (Wu et al . 2018), and fragments per kilobase exon model per million mapped reads (FPKM) determined as described previously in Lau et al . (2018) with the one exception that the ‘Tanzania’ 30 DAT storage root sample was sub-sampled for 30 million reads.…”

Section: Methodsmentioning

confidence: 99%

“…(2018) with the one exception that the ‘Tanzania’ 30 DAT storage root sample was sub-sampled for 30 million reads. To provide a comparison of expression abundances in the roots to leaves, ‘Beauregard’ and ‘Tanzania’ plants were grown as described in Lau et al . (2018) for control conditions and RNA-seq libraries from leaves processed as described above.…”

Section: Methodsmentioning

confidence: 99%

Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population

Pereira

Gemenet

Mollinari

et al. 2019

Preprint

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ABSTRACTIn developing countries, the sweetpotato,Ipomoea batatas(L.) Lam. (2n= 6x= 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population (‘Beauregard’×‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly predicted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every cM position. Multiple interval mapping was performed using our R package QTLPOLY and detected a total of 41 QTL, ranging from one to ten QTL per trait. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions allowed us to characterize additive allele effects as well as to compute QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.

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Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance

Cited by 22 publications

References 72 publications

RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato

RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato

Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]

Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population

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