Martins Mônica Letícia Turibio, Sforça Danilo Augusto, Dos Santos Luís Paulo, Pimenta Ricardo José Gonzaga, Mancini Melina Cristina, Aono Alexandre Hild, Cardoso-Silva Cláudio Benício, Vautrin Sonia, Bellec Arnaud, Dos Santos Renato Vicentini, Bérgès Helene, da Silva Carla Cristina, de Souza Anete Pereira
Institute of Biology (IB), State University of Campinas (UNICAMP), Campinas, SP, Brazil.
Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (UNICAMP), Campinas, SP, Brazil.
BMC Genomics. 2024 Dec 18;25(1):1201. doi: 10.1186/s12864-024-11089-1.
Elucidating the intricacies of the sugarcane genome is essential for breeding superior cultivars. This economically important crop originates from hybridizations of highly polyploid Saccharum species. However, the large size (10 Gb), high degree of polyploidy, and aneuploidy of the sugarcane genome pose significant challenges to complete genome sequencing, assembly, and annotation. One successful strategy for identifying candidate genes linked to agronomic traits, particularly those associated with sugar accumulation, leverages synteny and potential collinearity with related species.
In this study, we explored synteny between sorghum and sugarcane. Genes from a sorghum Brix QTL were used to screen bacterial artificial chromosome (BAC) libraries from two Brazilian sugarcane varieties (IACSP93-3046 and SP80-3280). The entire region was successfully recovered, confirming synteny and collinearity between the species. Manual annotation identified 51 genes in the hybrid varieties that were subsequently confirmed to be present in Saccharum spontaneum. This study employed a multifaceted approach to identify candidate genes for sugar accumulation, including retrieving the genomic region of interest, performing a gene-by-gene analysis, analyzing RNA-seq data for internodes from Saccharum officinarum and S. spontaneum accessions, constructing a coexpression network to examine the expression patterns of genes within the studied region and their neighbors, and finally identifying differentially expressed genes (DEGs).
This comprehensive approach led to the discovery of three candidate genes potentially involved in sugar accumulation: an ethylene-responsive transcription factor (ERF), an ABA 8'-hydroxylase, and a prolyl oligopeptidase (POP). These findings could be valuable for identifying additional candidate genes for other important agricultural traits and directly targeting candidate genes for further work in molecular breeding.
阐明甘蔗基因组的复杂性对于培育优良品种至关重要。这种具有重要经济价值的作物起源于高度多倍体甘蔗属物种的杂交。然而，甘蔗基因组的巨大规模（10 Gb）、高度的多倍性和非整倍性给全基因组测序、组装和注释带来了重大挑战。一种成功的策略是利用与相关物种的同线性和潜在共线性来鉴定与农艺性状相关的候选基因，特别是那些与糖分积累相关的基因。
在本研究中，我们探索了高粱和甘蔗之间的同线性。利用来自高粱糖分含量数量性状位点（Brix QTL）的基因筛选了两个巴西甘蔗品种（IACSP93 - 3046和SP80 - 3280）的细菌人工染色体（BAC）文库。整个区域被成功找回，证实了这两个物种之间的同线性和共线性。人工注释在杂交品种中鉴定出51个基因，随后证实这些基因存在于野生甘蔗中。本研究采用多方面的方法来鉴定糖分积累的候选基因，包括检索感兴趣的基因组区域、进行逐个基因分析、分析甘蔗和野生甘蔗节间的RNA测序数据、构建共表达网络以检查研究区域内及其邻近基因的表达模式，最后鉴定差异表达基因（DEG）。
这种综合方法导致发现了三个可能参与糖分积累的候选基因：一个乙烯响应转录因子（ERF）、一个ABA 8'-羟化酶和一个脯氨酰寡肽酶（POP）。这些发现对于鉴定其他重要农业性状的额外候选基因以及直接针对候选基因进行分子育种的进一步研究可能具有重要价值。
