Start Codon Region-related Polymorphism (SCRP): A Novel DNA Marker Technique for Assessing Genetic Diversity in Alfalfa Germplasm Collections

doi:10.7677/ynzwyj201312023

Abstract

Abstract:

Mostly PCRbased molecular markers amplified noncoding regions, or the whole genome randomly, the locus is far away from the gene of targeted trait. We developed a novel marker technique called start codon regionrelated polymorphism (SCRP) aimed for the amplification of gene start condon regions. It is based on the use of two primers of 18 nucleotides. The forward primer is designed from the targeted “Kozak” sequence; and the other primer, the reverse primer is an arbitrary sequence with an ATrich core to anneal with an intron. PCR amplification is applied for the first 5 cycles with an annealing temperature of 35℃, followed by 35 cycles with an annealing tempe-rature of 50℃. In the present study, we utilized SCRP to study genetic diversity of 34 alfalfa cultivars (varieties). Each PCR reaction has generated as many as 3 to 16 fragments of 50 to 2000bp in size. The successful genetic diversity of 34 alfalfa cultivars by SCRP was achieved. This new technique should be useful in genotyping germplasm collections and in tagging genes govern desirable agronomic traits of crop plants.

Key words: Genetic diversity, Medicago sativa, Start Codon Region-related Polymorphism

摘要：

目前广泛使用的基于PCR基础的分子标记多为扩增非编码区域，或是随机基因组中扩增，在QTL定位中得到的位点一般与目标性状基因距离较远，我们开发了一个新的基于启动子序列目的基因型分子标记技术——启动子区域相关序列多态性（SCRP），试图使标记能够更为准确的反映不同品种的遗传基础。它利用启动子位置保守一致序列（“Kozak”序列）作为其上游引物，利用内含子富含“AATT”的特性，作为核心序列设计下游引物，上下游引物均为18bp，引物间通过组合配对的方式作为扩增引物对。设计了14条上游引物和10条下游引物，共140对引物组合，对34个苜蓿品种进行扩增，研究了34个苜蓿的遗传多样性。每个PCR反应产生3~16个50~2000bp的条带，结果表明该标记简单、可靠、具有较高多态性，并且扩增区域为一种目的基因型分子标记，在种质资源研究中具有重要价值。

关键词: 遗传多样性, 苜蓿, 起始密码子区域相关序列多态性

CLC Number:

Q 75
Q 16

HE Qing-Yuan-, LI Zheng-Peng-, WU Ping-, YANG Hong-Yan-, WANG Song-Hua. Start Codon Region-related Polymorphism (SCRP): A Novel DNA Marker Technique for Assessing Genetic Diversity in Alfalfa Germplasm Collections[J]. Plant Diversity, 2013, 35(1): 48-54.

何庆元1、2, 李正鹏1, 吴萍1, 杨红燕2, 王松华1. 起始密码子区域相关序列多态性的开发及在苜蓿遗传多样性上的应用[J]. Plant Diversity, 2013, 35(1): 48-54.

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