Genetic diversity and population structure of Indonesia’s mandarin citrus genotypes using simple sequence repeat and start codon targeted markers

IF 1.6 3区农林科学 Q2 AGRONOMY

Genetic Resources and Crop Evolution Pub Date : 2024-08-24 DOI:10.1007/s10722-024-02130-z

Kristianto Nugroho, Tri Joko Santoso, Mia Kosmiatin, Dewi Sukma, Agus Purwito, Ali Husni, Reflinur Reflinur, Puji Lestari

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Abstract

Citrus is one of the prominent horticultural crops that is highly consumed by people around the world. Being located near the equator, Indonesia has several mandarin citrus genotypes, including siam and keprok citrus, which remain poorly characterized. Hence, assessing of their genetic diversity will help us identify genotypes that possess important traits suitable for breeding programs. The objective of this study were to analyze the genetic diversity of Indonesia’s local mandarin citrus genotypes using Simple Sequence Repeat (SSR) and Start Codon Targeted (SCoT) markers and compare the robustness of those markers in genetic diversity analysis. Thirty-seven mandarin genotypes consisting of 7 siam cultivars, 28 keprok cultivars, and 2 cultivars derived from their hybridization, were subjected to genetic diversity analysis using 20 SSR and SCoT markers. The number of alleles detected by SCoT markers was higher than by SSR markers. SCoT markers accounted for 119 alleles, while SSR markers accounted for 99 alleles. The number of alleles at each locus detected by SCoT and SSR markers varied from 4 to 9 and 2 to 7, respectively. In addition, 15 SCoT and 13 SSR markers with Polymorphic Information Content (PIC) values greater than 0.5 were identified, which indicated their potential as highly informative markers in citrus breeding programs. The phylogenetic tree and principal coordinate analysis (PCoA) plot constructed from SSR and SCoT markers revealed differentiation between the siam and keprok cultivars. The analysis of molecular variance (AMOVA) results indicated that there was greater genetic variation within populations than among populations, thus suggesting extensive cross-pollination in the citrus genotypes studied. The population structure, as indicated by the highest delta K value of K = 2 in SSR markers and K = 3 in SCoT markers, showed evidence of gene flow occurred among citrus populations. The findings have implication for future citrus breeding.

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利用简单序列重复和起始密码子目标标记分析印度尼西亚柑橘基因型的遗传多样性和种群结构

柑橘是重要的园艺作物之一，深受世界各地人们的喜爱。印度尼西亚地处赤道附近，拥有多个柑橘基因型，包括 siam 柑橘和 keprok 柑橘。因此，对它们的遗传多样性进行评估将有助于我们确定具有重要性状的基因型，以适合育种计划。本研究旨在利用简单序列重复（SSR）和起始密码定向（SCoT）标记分析印度尼西亚当地柑橘基因型的遗传多样性，并比较这些标记在遗传多样性分析中的稳健性。利用 20 个 SSR 和 SCoT 标记对 37 个柑橘基因型进行了遗传多样性分析，其中包括 7 个 Siam 栽培品种、28 个 keprok 栽培品种和 2 个由它们杂交而来的栽培品种。SCoT 标记检测到的等位基因数量高于 SSR 标记。SCoT 标记检测到 119 个等位基因，而 SSR 标记检测到 99 个等位基因。SCoT 和 SSR 标记在每个位点上检测到的等位基因数分别为 4 至 9 个和 2 至 7 个。此外，15 个 SCoT 标记和 13 个 SSR 标记的多态信息含量（PIC）值大于 0.5，这表明它们在柑橘育种计划中具有作为高信息量标记的潜力。根据 SSR 和 SCoT 标记构建的系统发生树和主坐标分析图显示了 siam 和 keprok 栽培品种之间的差异。分子方差分析（AMOVA）结果表明，种群内的遗传变异大于种群间的遗传变异，这表明所研究的柑橘基因型存在广泛的异花授粉。SSR 标记的最高 delta K 值为 K = 2，SCoT 标记的最高 delta K 值为 K = 3，这表明种群结构表明柑橘种群间存在基因流动。这些发现对未来柑橘育种具有重要意义。

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来源期刊

Genetic Resources and Crop Evolution 农林科学-农艺学

CiteScore

4.10

自引率

10.00%

发文量

178

审稿时长

3 months

期刊介绍： Genetic Resources and Crop Evolution is devoted to all aspects of plant genetic resources research. It publishes original articles in the fields of taxonomical, morphological, physiological, biochemical, genetical, cytological or ethnobotanical research of genetic resources and includes contributions to gene-bank management in a broad sense, that means to collecting, maintenance, evaluation, storage and documentation. Areas of particular interest include: -crop evolution -domestication -crop-weed relationships -related wild species -history of cultivated plants including palaeoethnobotany. Genetic Resources and Crop Evolution also publishes short communications, e.g. newly described crop taxa, nomenclatural notes, reports of collecting missions, evaluation results of gene-bank material etc. as well as book reviews of important publications in the field of genetic resources. Every volume will contain some review articles on actual problems. The journal is the internationalized continuation of the German periodical Die Kulturpflanze, published formerly by the Institute of Plant Genetics and Crop Plant Research at Gatersleben, Germany. All contributions are in the English language and are subject to peer reviewing.