Identification of QTLs for Starch Content in Sweetpotato (Ipomoea batatas (L.) Lam.)

Yu, Xiaoxia; Zhao, Ning; Li, Hui; Qin, Jie; Zhai, Hong; He, Shao-zhen; Li, Qiang; Liu, Qingchang

doi:10.1016/s2095-3119(13)60357-3

Cited by 18 publications

(15 citation statements)

References 6 publications

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“…Further, 219 out of 280 primers were polymorphic and produced a digital PCR fragment in sweetpotato that differed by at least 3-bp compared to the homologous product in beach morning glory. SSR markers have contributed to addressing the origins of sweetpotato [ 72 ] and to identification of loci involved in quantitative traits [ 73 ]. The identified cross-species transferable microsatellite markers from the present study might provide further insights into the origins of sweetpotato.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome Profiling of Beach Morning Glory (Ipomoea imperati) under Salinity and Its Comparative Analysis with Sweetpotato

et al. 2016

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The response and adaption to salt remains poorly understood for beach morning glory [Ipomoea imperati (Vahl) Griseb], one of a few relatives of sweetpotato, known to thrive under salty and extreme drought conditions. In order to understand the genetic mechanisms underlying salt tolerance of a Convolvulaceae member, a genome-wide transcriptome study was carried out in beach morning glory by 454 pyrosequencing. A total of 286,584 filtered reads from both salt stressed and unstressed (control) root and shoot tissues were assembled into 95,790 unigenes with an average length of 667 base pairs (bp) and N50 of 706 bp. Putative differentially expressed genes (DEGs) were identified as transcripts overrepresented under salt stressed tissues compared to the control, and were placed into metabolic pathways. Most of these DEGs were involved in stress response, membrane transport, signal transduction, transcription activity and other cellular and molecular processes. We further analyzed the gene expression of 14 candidate genes of interest for salt tolerance through quantitative reverse transcription PCR (qRT-PCR) and confirmed their differential expression under salt stress in both beach morning glory and sweetpotato. The results comparing transcripts of I. imperati against the transcriptome of other Ipomoea species, including sweetpotato are also presented in this study. In addition, 6,233 SSR markers were identified, and an in silico analysis predicted that 434 primer pairs out of 4,897 target an identifiable homologous sequence in other Ipomoea transcriptomes, including sweetpotato. The data generated in this study will help in understanding the basics of salt tolerance of beach morning glory and the SSR resources generated will be useful for comparative genomics studies and further enhance the path to the marker-assisted breeding of sweetpotato for salt tolerance.

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Section: Resultsmentioning

confidence: 99%

Transcriptome Profiling of Beach Morning Glory (Ipomoea imperati) under Salinity and Its Comparative Analysis with Sweetpotato

et al. 2016

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“…(covered 5,792 cM with an average marker distance of 4.5 cM). For dry-matter (Zhao et al 2013) and starch (Yu et al 2014), two parental maps were based on AFLP and SSR markers ordered into 90 LGs for Xushu 18 (covered 8,184.5 cM with an average marker distance of 3.9 cM) and 90…”

Section: Discussionmentioning

confidence: 99%

“…They constructed two parental maps consisted of 726 and 947 single-dose AFLP markers ordered into 90 and 86 linkage groups (LGs) for Beauregard and Tanzania, respectively (Cervantes-Flores et al 2008). For dry-matter (Zhao et al 2013) and starch (Yu et al 2014), two parental maps were constructed consisted of 2077 markers (1936 AFLP and 141 SSR) and 1954 markers (1824 AFLP and 130 SSR) ordered into 90 LGs for Xushu 18 and 90 LGs for Xu 781. These markers, however, are still not enough to evenly cover the 90 chromosomes of sweetpotato.…”

Section: Introductionmentioning

confidence: 99%

QTL analysis and GWAS of agronomic traits in sweetpotato (<i>Ipomoea batatas</i> L.) using genome wide SNPs

et al. 2020

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While sweetpotato (Ipomoea batatas L.) improvement has generally been done by field-based selection, molecular genetic studies on traits of interest, i.e., molecular markers are needed for enhancing the breeding program of this world's 7 th most important crop, as such markers facilitate marker-assisted selection. Here, we performed a combined approach of QTLs analyses and GWAS of storage root β-carotene content (BC), dry-matter (DM) and starch content (SC) using the genetic linkage maps constructed with 5,952 and 5,640 SNPs obtained from F 1 progenies between cultivars 'J-Red' and 'Choshu'. BC was negatively correlated with DM (r =-0.45) and SC (r =-0.51), while DM was positively correlated with SC (r = 0.94). In both parental maps, a total of five, two and five QTL regions on linkage groups 7 and 8 were associated with BC, DM and SC, respectively. In GWAS of BC, one strong signal (P = 1.04 × 10-9) was observed on linkage group 8, which co-located with one of the above QTL regions. The SNPs markers found here, particularly for βcarotene, would be useful base resources for future marker-assisted selection program with this trait.

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“…A recent map was developed from a selfing population and used only single-dose SNPs, resulting in higher marker saturation in comparison to the previous maps (Shirasawa et al 2017), though the map was still not integrated. In some of these cases, QTL mapping analyses were performed for several traits, related mostly to quality (Cervantes-Flores et al 2011;Zhao et al 2013;Yu et al 2014;Kim et al 2017) and resistance to biotic stresses (Cervantes-Flores et al 2008b;Yada et al 2017a). For yield-related traits, only two studies have been reported to date (Chang et al 2009;Li et al 2014).…”

Section: Qtl Mapping For Yield Traits In Sweetpotatomentioning

confidence: 99%

Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population

et al. 2020

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In 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 fit only 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 biparental population (‘Beauregard’ × ‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted 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 centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits, and provided a basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into additive allele effects and were used to compute multiple 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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Identification of QTLs for Starch Content in Sweetpotato (Ipomoea batatas (L.) Lam.)

Cited by 18 publications

References 6 publications

Transcriptome Profiling of Beach Morning Glory (Ipomoea imperati) under Salinity and Its Comparative Analysis with Sweetpotato

Transcriptome Profiling of Beach Morning Glory (Ipomoea imperati) under Salinity and Its Comparative Analysis with Sweetpotato

QTL analysis and GWAS of agronomic traits in sweetpotato (<i>Ipomoea batatas</i> L.) using genome wide SNPs

Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population

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