Disentangling the Origins of Cultivated Sweet Potato (Ipomoea batatas (L.) Lam.)

Sweet potato (Ipomoea batatas (L.) Lam., Convolvulaceae) counts among the most widely cultivated staple crops worldwide, yet the origins of its domestication remain unclear. This hexaploid species could have had either an autopolyploid origin, from the diploid I. trifida, or an allopolyploid origin, involving genomes of I. trifida and I. triloba. We generated molecular genetic data for a broad sample of cultivated sweet potatoes and its diploid and polyploid wild relatives, for noncoding chloroplast and nuclear ITS sequences, and nuclear SSRs. Our data did not support an allopolyploid origin for I. batatas, nor any contribution of I. triloba in the genome of domesticated sweet potato. I. trifida and I. batatas are closely related although they do not share haplotypes. Our data support an autopolyploid origin of sweet potato from the ancestor it shares with I. trifida, which might be similar to currently observed tetraploid wild Ipomoea accessions. Two I. batatas chloroplast lineages were identified. They show more divergence with each other than either does with I. trifida. We thus propose that cultivated I. batatas have multiple origins, and evolved from at least two distinct autopolyploidization events in polymorphic wild populations of a single progenitor species. Secondary contact between sweet potatoes domesticated in Central America and in South America, from differentiated wild I. batatas populations, would have led to the introgression of chloroplast haplotypes of each lineage into nuclear backgrounds of the other, and to a reduced divergence between nuclear gene pools as compared with chloroplast haplotypes.甘薯（Ipomoea batatas (L.) Lam.，旋花科Convolvulaceae）是全球范围内广泛种植的主粮作物之一，但其驯化起源至今仍未明确。该六倍体物种的起源存在两种潜在假说：一是由二倍体三裂叶薯（I. trifida）经同源多倍化演化而来；二是由三裂叶薯（I. trifida）与远轴叶薯（I. triloba）的基因组经异源多倍化形成。本研究针对栽培甘薯及其二倍体、多倍体野生近缘类群的广泛样本，获取了非编码叶绿体序列、细胞核核糖体DNA内转录间隔区（ITS）以及核简单序列重复（SSRs）的分子遗传学数据。研究结果不支持甘薯为异源多倍体起源的假说，同时未发现远轴叶薯（I. triloba）对栽培甘薯基因组存在任何遗传贡献。三裂叶薯（I. trifida）与甘薯亲缘关系密切，但二者并不共享单倍型。本研究数据支持甘薯的同源多倍体起源假说：其祖先与三裂叶薯（I. trifida）共享共同祖先，该类群或与当前已报道的四倍体野生番薯属（Ipomoea）种质资源相似。本研究共鉴定出两类甘薯叶绿体谱系，这两类谱系之间的序列分化程度均高于其各自与三裂叶薯（I. trifida）的分化程度。据此我们提出，栽培甘薯存在多起源路径，即由单个祖先物种的多态性野生种群中至少两次独立的同源多倍化事件演化而来。在中美洲和南美洲分别驯化的栽培甘薯，均源自分化的野生甘薯种群；二者的二次基因交流，会导致两类叶绿体单倍型在彼此的核基因组背景中发生渐渗，进而使得核基因库之间的分化程度低于叶绿体单倍型之间的分化程度。