Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement (original) (raw)
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Gates Open Research
Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the speci...
Sweetpotato (Ipomoea batatas(L.) Lam) is the world’s seventh most important food crop by production quantity. Cultivated sweetpotato is a hexaploid (2n = 6x = 90), and its genome (B1B1B2B2B2B2) is quite complex due to polyploidy, self-incompatibility, and high heterozygosity. Here we established a haploid-resolved and chromosome-scalede novoassembly of autohexaploid sweetpotato genome sequences. Before constructing the genome, we created chromosome-scale genome sequences inI. trifidausing a highly homozygous accession, Mx23Hm, with PacBio RSII and Hi-C reads. Haploid-resolved genome assembly was performed for a sweetpotato cultivar, Xushu18 by hybrid assembly with Illumina paired-end (PE) and mate-pair (MP) reads, 10X genomics reads, and PacBio RSII reads. Then, 90 chromosome-scale pseudomolecules were generated by aligning the scaffolds onto a sweetpotato linkage map.De novoassemblies were also performed for chloroplast and mitochondrial genomes inI. trifidaand sweetpotato. In tota...
Theoretical and Applied Genetics
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 F1 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 c...
Development of genetic and genomic resources for breeding improved sweetpotato
Production of sweetpotato (Ipomoea batatas L. (Lam)), an important staple food in Sub-Saharan Africa, is limited by a number of constraints, such as low adaptability of available varieties and landraces, virus diseases, insect pests and drought. Consequently, yields achieved by resource-poor farmers in SSA are low. Improved and well adapted sweetpotato varieties with increased tolerance to biotic and abiotic stresses could significantly contribute to augment productivity and, once available, would have a large positive impact on food and income security in Sub-Saharan Africa. However, breeding efforts are limited by the crop's genetic complexity, lack of information about its genetic resources and access to genomics tools for this crop for modern breeding. To mobilize allelic diversity and to facilitate introgression of desirable alleles into breeding populations, we have established genetic and genomics tools including a well defined Composite Genotype Set and a gene index. Furthermore we have designed and tested more than 200 new microsatellite markers and identified 200 SNP markers in stress response genes. A sweetpotato DArT marker system is under development. For establishing the gene index, we applied Next Generation sequencing technologies to characterize the sweetpotato transcriptome. The index comprises 31.165 contigs and 29.080 singletons and was annotated based on sequence comparisons with known proteins. The Composite Genotype Set and the genomics tools will support trait capture efforts on molecular level, will improve the allelic diversity for breeding Sweetpotato, genetic resources, transcriptome, molecular marker. me security of resource-poor farmers in Sub-Saharan Africa. e 100 published SSR markers (Hu et al. 2004, Arizio et al. 2008). Additional genomic understanding of the sweetpotato gene pools and finally will enhance access to improved varieties.
BMC Genomics, 2010
Background: Sweetpotato (Ipomoea batatas (L.) Lam.), a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpotato is in striking contrast to its importance for human nutrition. Previously existing sequence data were restricted to around 22,000 expressed sequence tag (EST) sequences and~1,500 GenBank sequences. We have used 454 pyrosequencing to augment the available gene sequence information to enhance functional genomics and marker design for this plant species. Results: Two quarter 454 pyrosequencing runs used two normalized cDNA collections from stems and leaves from drought-stressed sweetpotato clone Tanzania and yielded 524,209 reads, which were assembled together with 22,094 publically available expressed sequence tags into 31,685 sets of overlapping DNA segments and 34,733 unassembled sequences. Blastx comparisons with the UniRef100 database allowed annotation of 23,957 contigs and 15,342 singletons resulting in 24,657 putatively unique genes. Further, 27,119 sequences had no match to protein sequences of UniRef100database. On the basis of this gene index, we have identified 1,661 gene-based microsatellite sequences, of which 223 were selected for testing and 195 were successfully amplified in a test panel of 6 hexaploid (I. batatas) and 2 diploid (I. trifida) accessions.
Background: Sweetpotato (Ipomoea batatas (L.) Lam.), a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpotato is in striking contrast to its importance for human nutrition. Previously existing sequence data were restricted to around 22,000 expressed sequence tag (EST) sequences and~1,500 GenBank sequences. We have used 454 pyrosequencing to augment the available gene sequence information to enhance functional genomics and marker design for this plant species. Results: Two quarter 454 pyrosequencing runs used two normalized cDNA collections from stems and leaves from drought-stressed sweetpotato clone Tanzania and yielded 524,209 reads, which were assembled together with 22,094 publically available expressed sequence tags into 31,685 sets of overlapping DNA segments and 34,733 unassembled sequences. Blastx comparisons with the UniRef100 database allowed annotation of 23,957 contigs and 15,342 singletons resulting in 24,657 putatively unique genes. Further, 27,119 sequences had no match to protein sequences of UniRef100database. On the basis of this gene index, we have identified 1,661 gene-based microsatellite sequences, of which 223 were selected for testing and 195 were successfully amplified in a test panel of 6 hexaploid (I. batatas) and 2 diploid (I. trifida) accessions.
The draft genomes of five agriculturally important African orphan crops
GigaScience
Background: The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few
Scientific Reports
The discovery of the insertion of IbT-DNA1 and IbT-DNA2 into the cultivated (hexaploid) sweetpotato [Ipomoea batatas (L.) Lam.] genome constitutes a clear example of an ancient event of Horizontal Gene Transfer (HGT). However, it remains unknown whether the acquisition of both IbT-DNAs by the cultivated sweetpotato occurred before or after its speciation. Therefore, this study aims to evaluate the presence of IbT-DNAs in the genomes of sweetpotato's wild relatives belonging to the taxonomic group series Batatas. Both IbT-DNA1 and IbT-DNA2 were found in tetraploid I. batatas (L.) Lam. and had highly similar sequences and at the same locus to those found in the cultivated sweetpotato. Moreover, IbT-DNA1 was also found in I. cordatotriloba and I. tenuissima while IbT-DNA2 was detected in I. trifida. This demonstrates that genome integrated IbT-DNAs are not restricted to the cultivated sweetpotato but are also present in tetraploid I. batatas and other related species. The sweetpotato [6X Ipomoea batatas (L.) Lam] is a member of the genus Ipomoea, the largest genus in the morning glory (Convolvulaceae) family. This family contains approximately 50 genera and more than 1,000 species. Over half of these species are concentrated in the Americas, where they are distributed as cultigens, medicinal plants and weeds 1. Among the morning glories, I. batatas is the only species with an economic importance as a major food crop 2 , although I. aquatica is also cultivated and consumed as a leafy vegetable, mainly in SouthEast Asia. Series Batatas is a subdivision within the genus Ipomoea. This is a relatively young clade that diversified circa 12 million years ago 3. This group includes the cultivated hexaploid sweetpotato [I. batatas (L.) Lam], the tetraploid (4x) sweetpotato I. batatas (L.) Lam 4 , and 13 other species considered to be the wild relatives of the cultivated sweetpotato. These wild relatives are I. cordatotriloba, I. cynanchifolia, I. grandiflora, I. lacunosa, I. leucantha, I. littoralis, I. ramosissima, I. splendor sylvae (previously named umbraticola), I. tabascana, I. tenuissima, I. tiliacea, I. trifida and I. triloba 5,6. Members of the series Batatas are endemic to the Americas, except I. littoralis that is native to Madagascar, South and Southeast Asia, Australia, and the Pacific region 5. The basic chromosome number of the series Batatas species is 2n = 2 × = 30. While most species are diploid (2x), several are tetraploid (4x) or hexaploid (6x) 7. To avoid confusion, hereafter in the current text, the (6x) sweetpotato (I. batatas) will be referred to as Ib6x, the tetraploid form of I. batatas as Ib4x, and the combination of both as "the sweetpotato group". The sweetpotato is a crop native to the Americas and it was an important food crop for the Inca and Mayan cultures. Its origin and center(s) of genetic diversity have been proposed as somewhere between the Yucatan Peninsula of Mexico and the mouth of the Orinoco River in Venezuela 8,9 , Peru and Ecuador 9. Papua New Guinea, Indonesia and the Philippines are suggested as secondary centers of diversity 10. Today, sweetpotato is a major staple food in numerous tropical countries 11. However, its botanical origin and details about its domestication remain under debate.