InDel markers: An extended marker resource for molecular breeding in chickpea
InDel markers: An extended marker resource for molecular breeding in chickpea
复制标题
DOI：
10.1371/journal.pone.0213999
复制
发表时间：
2019-03-18
期刊：
影响因子：
3.7
通讯作者：
Varshney, Rajeev K.
中科院分区：
文献类型：
--
作者：
Jain, Ankit;Roorkiwal, Manish;Varshney, Rajeev K.
鹰嘴豆是最重要的豆类食品之一，是满足全球不断增长的食品和营养需求的关键。为了在作物改良计划中部署分子育种方法，用户友好且具有成本效益的标记资源仍然是先决条件。下一代测序 (NGS) 技术的出现导致了数千个标记的生成，作为多个大规模基因组测序和重测序计划的一部分。最近，基于 PCR 的插入缺失 (InDels) 因其共显性、廉价和高度多态性而成为一种流行的基于凝胶的基因分型解决方案。为了扩大鹰嘴豆基因组辅助育种 (GAB) 的标记资源，使用在一个种间 (ICC 4958 x PI 489777) 和两个种内 (ICC 283 x ICC 8261 和 ICC 4958 x ICC 1882) 作图群体的 5 个亲本系上生成的全基因组重测序数据来识别 InDels。使用 Dindel 软件和默认参数共识别出 231,658 个 InDels。此外，总共有 8,307 个 InDels。选择 20 bp 大小用于开发基于凝胶的标记，其中可以为 7,523 个（90.56%）标记设计引物。平均而言，标记出现的频率为 1,038 个 InDels/LG，其中 CaLG04 上的标记数量最多（1,952 个 InDels），CaLG08 上的标记数量最少（360 个 InDels）。为了验证这些 InDels，随机选择了总共 423 个引物对并在选定的亲本系上进行测试。在 3% 琼脂糖凝胶上观察到亲本的多态性率为 46.06% 至 58.01%，扩增率为 80%。这项研究清楚地反映了现有序列数据对于鹰嘴豆全基因组 InDels 开发的有用性，这可以进一步促进和加速鹰嘴豆的广泛遗传和分子育种活动。
Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 x PI 489777) and two intra-specific (ICC 283 x ICC 8261 and ICC 4958 x ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with. 20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea.