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Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces 'Gigantes' and 'Elephantes' Reveals Rich Functional Variation.
Biochemical Genetics ( IF 2.4 ) Pub Date : 2019-04-17 , DOI: 10.1007/s10528-019-09920-6
Aliki Xanthopoulou 1 , Christos Kissoudis 2 , Ifigeneia Mellidou 3 , Maria Manioudaki 4 , Irene Bosmali 1 , Vasilis Tsakonitis 3 , Apostolos Kalivas 3 , Maslin Osathanunkul 5, 6 , Athanasios Tsaftaris 2 , Ioannis Ganopoulos 3 , Panagiotis Madesis 1
Affiliation  

Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, ‘Gigantes’ and ‘Elephantes’ phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for ‘Gigantes’ and ‘Elephantes,’ respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in ‘Elephantes’ and 648 upregulated in ‘Gigantes.’ A significant upregulation of defense-related genes was observed in ‘Elephantes,’ among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in ‘Gigantes’ and ‘Elephantes,’ respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in ‘Gigantes’ and 40.1% in ‘Elephantes’ of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.

中文翻译:

扩大菜豆的基因组资源:从头转录组的组装和地方品种“ Gigantes”和“ Elephantes”的分析揭示了丰富的功能变异。

豆类是世界上最重要的主粮之一。与普通豆(菜豆)相比,红花菜豆(菜豆)是一种小型农业作物。豆子已从中美洲传入欧洲,并从那时起一直散布到不同的地理区域。这导致了许多具有显着特征和适应潜力的地方品种和地方品种的产生。为了鉴定和表征两个密切相关的红花菜豆栽培品种的潜在基因组变异,我们在两个美洲锥land地方品种中进行了具有从头转录组组装的RNA-Seq ,“ Gigantes”和“ Elephantes”的表型不同,种子大小和形状也不同。清除的读物分别为“ Gigantes”和“ Elephantes”生成了37,379和37,774笔成绩单。在两个品种之间共鉴定出1896个DEG,其中“象皮”中上调1248个,而“巨人”中上调648个。在“大象”中观察到防御相关基因的显着上调,其中包括AP2-EREBPWRKYNACbHLH的许多成员转录因子家族。总共在“ Gigantes”和“ Elephantes”中识别出3956和4322 SSR。三核苷酸重复是最主要的重复基序,在所鉴定的SSR的“ Gigantes”中占41.9%,在“ Elephantes”中占40.1%,其次是二核苷酸重复(两个品种中均占29.1%)。此外,鉴定出19281个推定的SNP,其中3161个不是同义的,因此具有潜在的功能含义。高可信度的非同义SNP的成功与HRM分析,可直接通过了验证P球菌分子育种。这些结果显着扩大了球状疟原虫内多态性标记的数量属,能够可靠地鉴定红花菜豆的品种,构建高分辨率的遗传图谱,加强全基因组的关联研究。它们最终为改善紧密相关和可交配的菜豆的遗传储藏做出了贡献。
更新日期:2019-04-17
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