Abstract
Sweet potato, a dicotyledonous and perennial plant, is the third tuber/root crop species behind potato and cassava in terms of production. Long terminal repeat (LTR) retrotransposons are highly abundant in sweet potato, contributing to genetic diversity. Retrotransposon-based insertion polymorphism (RBIP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there have been no transposon marker-based genetic diversity analyses of sweet potato. Here, we reported a structure-based analysis of the sweet potato genome, a total of 21555 LTR retrotransposons, which belonged to the main LTR-retrotransposon subfamilies Ty3-gypsy and Ty1-copia were identified. After searching and selecting using Hidden Markov Models (HMMs), 1616 LTR retrotransposon sequences containing at least two models were screened. A total of 48 RBIP primers were synthesized based on the high copy numbers of conserved LTR sequences. Fifty-six amplicons with an average polymorphism of 91.07% were generated in 105 sweet potato germplasm resources based on RBIP markers. A Unweighted Pair Group Method with Arithmatic Mean (UPGMA) dendrogram, a model-based genetic structure and principal component analysis divided the sweet potato germplasms into 3 groups containing 8, 53, and 44 germplasms. All the three analyses produced significant groupwise consensus. However, almost all the germplasms contained only one primary locus. The analysis of molecular variance (AMOVA) among the groups indicated higher intergroup genetic variation (53%) than intrapopulation genetic variation. In addition, long-term self-retention may cause some germplasm resources to exhibit variable segregation. These results suggest that these sweet potato germplasms are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the utility of RBIP markers for determining the intraspecies variability of sweet potato and have the potential to be used as core primer pairs for variety identification, genetic diversity assessment and linkage map construction. The results could provide a good theoretical reference and guidance for germplasm research and breeding.
Highlights
Sweet potato (Ipomoea batatas (L.) Lam.) is regarded as the world’s seventh most important food crop and can be used as a staple food, animal feed, industrial raw material to extract starch as well as in alcohol and biofuel
Several morphological and molecular markers have been developed to assess the genetic diversity of sweet potato germplasm, including random amplified polymorphic DNAs (RAPDs)[3,4,5], amplified fragment length polymorphisms (AFLPs)[6,7] (Li et al, 2009; Liu et al, 2012), simple sequence repeats (SSRs)[8,9,10], and single nucleotide polymorphisms (SNPs)[2]
According to the sequence similarity with the reported retrotransposons, 13002 Long terminal repeat (LTR) retrotransposons were assigned to the copia family, 8114 LTR retrotransposons belonged to the gypsy family, and 439 LTR retrotransposons were classified to other families
Summary
Sweet potato (Ipomoea batatas (L.) Lam.) is regarded as the world’s seventh most important food crop and can be used as a staple food, animal feed, industrial raw material to extract starch as well as in alcohol and biofuel. Several types of retrotransposon-based DNA markers have been developed and widely applied in evaluating genetic diversity and constructing linkage maps of numerous plant species[1,17,18,19,20,21,22,23,24]. We report the development of new retrotransposon-based insertion polymorphism markers (RBIPs) derived from the genome sequence of the sweet potato cultivar Taizhong No 6 (China national accession number 2013003) and evaluated the capacity and efficiency of these markers for distinguishing genetic diversity in 105 cultivars. The primary objective of this work is to provide new insights into the classification of sweet potato and to assist in the genetic research and breeding of sweet potato
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