Diversity and structure assessment of the genetic resources in a germplasm collection from a vanilla breeding programme in Madagascar

IF 1.2 4区生物学 Q3 PLANT SCIENCES

Plant Genetic Resources: Characterization and Utilization Pub Date : 2023-12-22 DOI:10.1017/s1479262123000631

Rivo Onisoa Léa Rasoamanalina, Khaled Mirzaei, M. El Jaziri, Angel Rafael Ramirez Ramirez, Pierre Bertin

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引用次数: 0

Abstract

A breeding programme of aromatic vanilla, dating back to 1944, was conducted in Ambohitsara, Antalaha, SAVA (Sambava, Antalaha, Vohemara, Andapa) – Madagascar. Imported, local, wild and cultivated vanillas were used as progenitors and thousands of hybrids were generated. However, this germplasm has not undergone any genetic evaluation, and it appears that these valuable genetic resources have been dispersed or lost after the end of the programme (2000). This study aims to investigate the genetic diversity and structure of rescued genotypes currently held in a local collection in Antalaha. Double digest restriction associated-site (RAD)-seq (ddRAD)-seq protocol was applied, providing 865 million read sequences from 56 accessions. The ddRAD sequences have been deposited to the SRA archive of NCBI. From the data, 23,701 filtered concordant common Single Nucleotide Polymorphisms (SNPs) were identified using the three widely used tools (Stacks, BCFtools, Genome Analysis ToolKit - GATK) for short-read library sequencing. These SNPs were used for germplasm evaluation. Clustering analysis segregated samples into five genetic groups: Vanilla planifolia, Vanilla pompona, hybrid Tsitaitra, Vanille Banane and the phenotype Tsivaky. Our analysis revealed distinct subgroups within V. pompona and Tsitaitra, emphasizing the importance of further characterization to accurately reflect the genetic diversity and facilitate better utilization of these accessions in future research and germplasm management. The presence of private alleles in all groups (from 487 to 2866) indicated that populations were diverging and represented a large gene pool that could be useful for future breeding efforts. The genetic data obtained from this study offers valuable insights into the genetic diversity and structure of the vanilla population, with potential applications in breeding and conservation efforts.

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马达加斯加香草育种计划种质资源的多样性和结构评估

早在 1944 年，马达加斯加就在安博希萨拉、安塔拉哈、SAVA（桑巴瓦、安塔拉哈、沃赫马拉、安达帕）开展了香草育种计划。进口的、当地的、野生的和栽培的香草被用作原种，并产生了数千个杂交种。然而，这些种质没有经过任何遗传评估，而且在该计划结束（2000 年）后，这些宝贵的遗传资源似乎已经散失或丢失。本研究旨在调查目前安塔拉哈当地收集的获救基因型的遗传多样性和结构。研究采用了双消化限制性相关位点（RAD）-测序（ddRAD）-测序协议，提供了来自 56 个登录品系的 8.65 亿读取序列。ddRAD 序列已存入 NCBI 的 SRA 档案库。从这些数据中，利用三种广泛使用的短线程文库测序工具（Stacks、BCFtools、Genome Analysis ToolKit - GATK）确定了 23,701 个筛选出的一致的常见单核苷酸多态性（SNPs）。这些 SNPs 被用于种质评估。聚类分析将样本分为五个基因组：Vanilla planifolia、Vanilla pompona、杂交种 Tsitaitra、Vanille Banane 和表型 Tsivaky。我们的分析揭示了 V. pompona 和 Tsitaitra 中不同的亚群，强调了进一步鉴定的重要性，以准确反映遗传多样性，促进在未来的研究和种质管理中更好地利用这些品种。所有群体（从 487 个到 2866 个）中都存在私有等位基因，这表明种群正在发生分化，并代表了一个庞大的基因库，可用于未来的育种工作。这项研究获得的遗传数据为了解香草种群的遗传多样性和结构提供了宝贵的信息，具有育种和保护工作的潜在应用价值。

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来源期刊

Plant Genetic Resources: Characterization and Utilization Agricultural and Biological Sciences-Agronomy and Crop Science

CiteScore

2.80

自引率

0.00%

发文量

审稿时长

>12 weeks

期刊介绍： Plant Genetic Resources is an international journal which provides a forum for describing the application of novel genomic technologies, as well as their integration with established techniques, towards the understanding of the genetic variation captured in both in situ and ex situ collections of crop and non-crop plants; and for the airing of wider issues relevant to plant germplasm conservation and utilisation. We particularly welcome multi-disciplinary approaches that incorporate both a technical and a socio-economic focus. Technical aspects can cover developments in technologies of potential or demonstrated relevance to the analysis of variation and diversity at the phenotypic and genotypic levels.