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Comparative Transcriptome Profiling Reveals the Genes Involved in Storage Root Expansion in Sweetpotato (Ipomoea batatas (L.) Lam.)

ABSTRACT: Sweetpotato (Ipomoea batatas (L.) Lam.) is recognized as one of the most important root crops in the world by the Food and Agriculture Organization of the United Nations. The yield of sweetpotato is closely correlated with the rate of storage root (SR) formation and expansion. At present, most of the studies on sweetpotato SR expansion are focused on the physiological mechanism. To explore the SR expansion mechanism of sweetpotato, we performed transcriptome sequencing of SR harvested at 60, 90, 120, and 150 days after planting (DAP) to analyze two sweetpotato lines, Xuzishu 8 and its crossing progenies named Xu 18-192, which were selected from an F1 segregation population of Xuzishu 8 and Meiguohong, in which SR expansion was delayed significantly. A total of 57,043 genes were produced using transcriptome sequencing, of which 1312 were differentially expressed genes (DEGs) in four SR growth periods of the sweetpotato lines. The combination of the KEGG and trend analysis revealed several key candidate genes involved in SR expansion. The SBEI gene involved in starch metabolism, and transcription factors ARF6, NF-YB3 and NF-YB10 were all significantly up-regulated during SR expansion. The data from this study provide insights into the complex mechanisms of SR formation and expansion in sweetpotato and identify new candidate genes for increasing the yield of sweetpotato.

SUBMITTER: Song W

PROVIDER: S-EPMC9321896 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundSweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to root rot have not yet been reported, and the biological mechanisms of resistance remain unclear in sweetpotato. Thus, increasing our knowledge about the mechanism of disease resistance and identifying resistance loci will assist in the development of disease resistance breeding.ResultsIn this study, we constructed genetic linkage maps of sweetpotato using a mapping population consisting of 300 individuals derived from a cross between Jizishu 1 and Longshu 9 by simple sequence repeat (SSR) markers, and mapped seven QTLs for resistance to root rot. In total, 484 and 573 polymorphic SSR markers were grouped into 90 linkage groups for Jizishu 1 and Longshu 9, respectively. The total map distance for Jizishu 1 was 3974.24?cM, with an average marker distance of 8.23?cM. The total map distance for Longshu 9 was 5163.35?cM, with an average marker distance of 9.01?cM. Five QTLs (qRRM_1, qRRM_2, qRRM_3, qRRM_4, and qRRM_5) were located in five linkage groups of Jizishu 1 map explaining 52.6-57.0% of the variation. Two QTLs (qRRF_1 and qRRF_2) were mapped on two linkage groups of Longshu 9 explaining 57.6 and 53.6% of the variation, respectively. Furthermore, 71.4% of the QTLs positively affected the variation. Three of the seven QTLs, qRRM_3, qRRF_1, and qRRF_2, were colocalized with markers IES43-5mt, IES68-6?fs**, and IES108-1?fs, respectively.ConclusionsTo our knowledge, this is the first report on the construction of a genetic linkage map for purple sweetpotato (Jizishu 1) and the identification of QTLs associated with resistance to root rot in sweetpotato using SSR markers. These QTLs will have practical significance for the fine mapping of root rot resistance genes and play an important role in sweetpotato marker-assisted breeding.

Project description:To better define the sweetpotato polyploidy, we sought to reconstruct phylogenies of its subgenomes based on hybridization networks that could trace reticulate lineages of differentiated homoeolog triplets of multiple single-copy genes. In search of such homoeolog triplets, we distinguished cDNA variants of 811 single-copy Conserved Ortholog Set II (COSII) genes from two sweetpotato clones into variation partitions specified by corresponding homologs from two I. trifida lines, I. tenuissima and I. littoralis using a phylogenetic partition method, and amplicon variants of the COSII-marker regions from 729 of these genes from two sweetpotato clones into putative homoeoallele groups using haplotype tree and the partition methods referenced by corresponding homologs from I. tenuissima. These analyses revealed partly or completely differentiated expressed-homoeologs and homoeologs from a majority of these genes with three important features. 1. Two variation types: the predominant interspecific variations (homoeoalleles), which are non-randomly clustered, differentially interspecifically conserved or sweetpotato-specific, and the minor intraspecific ones (alleles), which are randomly distributed mostly at non-interspecifically variable sites, and usually sweetpotato-specific. 2. A clear differentiation of cDNA variants of many COSII genes into the variation partition specified by I. tenuissima or I. littoralis from that by I. trifida. 3. Three species-homolog-specified and one sweetpotato-specific variation partitions among 293 different COSII cDNAs, and two or three out of the four partitions among cDNA variants of 306 COSII genes. We then constructed hybridization networks from two concatenations of 16 and 4 alignments of 8 homologous COSII cDNA regions each, which included three taxa of expressed homoeologs in a triple-partition combination from the 16 or 4 sweetpotato COSII genes and 5 taxa each of respective cDNA homologs from the three sweetpotato relatives and I. nil, and inferred a species tree embodying both networks. The species tree predicted close-relative origins of three partly differentiated sweetpotato subgenomes.

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Comparative Transcriptome Profiling Reveals the Genes Involved in Storage Root Expansion in Sweetpotato (Ipomoea batatas (L.) Lam.)

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