Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

First author: Jisen Zhang; Affiliations: Fujian Agriculture and Forestry University (福建农林大学): Fuzhou, China

Corresponding author: Ray Ming (明瑞光)

Modern sugarcanes (现代甘蔗) are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum (热带种甘蔗) with hardiness (坚韧性), disease resistance and ratooning (再生的) of Saccharum spontaneum (割手密). Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions (裂变) of 2 ancestral chromosomes followed by translocations (易位) to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

现代甘蔗是种间杂交形成的多倍体，其同时具有来自热带甘蔗种的高糖特性，以及来自割手密的坚韧、疾病抗性以及再生能力。本文对单倍体割手密AP85-441品种进行了全基因组测序，组装了32个染色体，由8组同源染色体构成，每组同源染色体含4条染色体，共编码了35525个基因。进一步的研究发现割手密中8个基础染色体是由原始的10条染色体其中的2条发生裂变，随后易位到其它4条染色体上所导致的。有意思的是，作者发现80%的与疾病抗性相关的核酸结合位点-编码基因分布在这4个发生重排的染色体上，而且51%分布在重排区域。对64株割手密个体的重测序研究发现重排区域存在平衡选择，从而保证了遗传多样性。现代甘蔗中渗入的割手密基因组序列在AP85-441品种的基因组上是随机分布的，说明在不同的割手密品种之间同源区段的随机重组。本文报道的高质量野生甘蔗基因组将有助于加速甘蔗的育种改良。

通讯：明瑞光（http://net.fafu.edu.cn/hist/13/f8/c6013a136184/page.htm）

个人简介：1991-1995年，美国夏威夷大学，植物遗传育种博士；1995-1998年，美国德州农工大学，博士后。

研究方向：植物性染色体的起源与进化；被子植物性别决定基因网络；木瓜与甘蔗基因组结构与功能；甘蔗生物产量超亲遗传的分子机理。

doi: https://doi.org/10.1038/s41588-018-0237-2

Journal: Nature Genetics

Published date: 08 October, 2018

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