Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, People's Republic of China.
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
BMC Plant Biol. 2019 Apr 1;19(1):119. doi: 10.1186/s12870-019-1708-z.
Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses.
Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development.
We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.
番薯（Ipomoea batatas（L.）Lam.）是世界上第七大重要作物，主要因其地下贮藏根（SR）而种植。由于其复杂的基因组结构，该物种的遗传研究一直受到缺乏高质量参考序列的阻碍。二倍体番薯 Ipomoea trifida 是番薯的最亲近的亲缘物和假定祖先，被认为是番薯的模式物种，包括遗传、细胞学和生理学分析。
在这里，我们生成了具有高杂合度（2.20%）的 SR 形成二倍体 I. trifida var. Y22 的染色体规模基因组序列。尽管染色体基序的共线性分析表明，在分离后，I. trifida 与 Ipomoea nil 共享保守的核型，但由于 LTR-反转录转座子的更有效消除和缺乏物种特异性的 LTR-RTs 扩增爆发，I. trifida 的基因组比 I. nil 小得多。与四个非 SR 形成物种的比较表明，β-淀粉酶基因家族的进化可能与 SR 形成有关。我们进一步通过基因表达谱和数量性状位点（QTL）作图研究了关键基因 BMY11（与β-淀粉酶 1 的同一性为 47.12%）与这一重要农艺性状的关系。结合 SR 形态和结构、基因表达谱和 qPCR 结果，我们推断 BMY11 产物在分裂淀粉颗粒方面的活性和被回收以合成更大颗粒，有助于淀粉积累和 SR 膨胀。此外，我们发现 BMY11、sporamin 蛋白以及参与碳水化合物代谢和木质部木质化的关键基因的表达模式与 SR 发育过程中的番薯相似。
我们通过组合方法构建了高度杂合的 I. trifida 的高质量基因组参考，该基因组能够更好地解析该物种的基因组特征和基因组进化。番薯 SR 发育基因可以在 I. trifida 中被鉴定出来，这些基因表现出相似的功能和模式，表明具有典型 SR 的二倍体 I. trifida var. Y22 可以被认为是研究番薯 SR 发育的理想模型。
