Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

Shan Wu ,Jan Kreuze ,Jim Leebens‐Mack ,Marc Ghislain ,C Robin Buell ,John Hamilton ,Honghe Sun ,Awais Khan ,Lachlan Coin ,Haiyan Wang ,Mercy Kitavi ,Bode A Olukolu ,Dorcus C Gemenet ,Jennifer E Schaff ,Xin Wang ,Grant T Godden ,Chenxi Zhou ,Kan Bao ,Emily Crisovan ,Xinsun Yang ,Norma C Manrique‐Carpintero ,Krystle Wiegert‐Rininger ,Chen Jiao ,G Craig Yencho ,Brieanne Vaillancourt ,Daifu Ma ,R.o.m Mwanga ,Kin H Lau ,Lauren A Eserman ,Qinghe Cao ,Wolfgang J Grüneberg ,Jiming Jiang ,Zhangjun Fei

doi:10.1038/s41467-018-06983-8

Abstract

Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. Agronomic improvement of sweetpotato has lagged behind other major food crops due to a lack of genomic and genetic resources and inherent challenges in breeding a heterozygous, clonally propagated polyploid. Here, we report the genome sequences of its two diploid relatives, I. trifida and I. triloba, and show that these high-quality genome assemblies are robust references for hexaploid sweetpotato. Comparative and phylogenetic analyses reveal insights into the ancient whole-genome triplication history of Ipomoea and evolutionary relationships within the Batatas complex. Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content. These resources will facilitate genome-enabled breeding in this important food security crop.

Highlights

Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa
We sequenced the genomes of I. trifida NCNSP0306 and I. triloba NCNSP0323, two diploid species closely related to the hexaploid sweetpotato (Fig. 1 and Supplementary Method 1)
Based on the 17-mer depth distribution of the Illumina reads (Supplementary Fig. 1), the I. trifida genome is 526.4 Mb with a heterozygosity level of 0.24% calculated from single nucleotide polymorphism (SNP) analyses

Summary

Introduction

Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. We report the genome sequences of its two diploid relatives, I. trifida and I. triloba, and show that these high-quality genome assemblies are robust references for hexaploid sweetpotato. Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content These resources will facilitate genomeenabled breeding in this important food security crop. To provide high-quality reference genome resources and further investigate the relationship between hexaploid sweetpotato and its diploid relatives, we generated high quality, chromosome-scale genome assemblies of I. trifida and I. triloba, resequenced 16 cultivars and landraces widely used in African breeding programs, and performed a suite of comparative genomic analyses. Our findings illustrate the utility of highquality diploid I. trifida and I. triloba genomes for genomeenabled breeding and research in this important food security crop

Methods

Results

Conclusion