Development and validation of simple sequence repeat markers from Arachis hypogaea transcript sequences
Houmiao Wang,
Yong Lei,
Liying Yan,
Liyun Wan,
Yan Cai,
Zefeng Yang,
Jianwei Lv,
Xiaojie Zhang,
Chenwu Xu,
Boshou Liao
Affiliations
Houmiao Wang
Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, CAAS-ICRISAT Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, China
Yong Lei
Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, CAAS-ICRISAT Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, China
Liying Yan
Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, CAAS-ICRISAT Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, China
Liyun Wan
Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, CAAS-ICRISAT Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, China
Yan Cai
Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, CAAS-ICRISAT Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, China
Zefeng Yang
Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Zhejiang, China
Jianwei Lv
Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, CAAS-ICRISAT Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, China
Xiaojie Zhang
Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, CAAS-ICRISAT Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, China
Chenwu Xu
Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Zhejiang, China
Boshou Liao
Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, CAAS-ICRISAT Joint Laboratory for Groundnut Aflatoxin Management, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, China
Simple sequence repeats (SSRs) are important molecular markers for assessing genetic diversity in Arachis hypogaea L. and many other crops and constructing genetic linkage maps for important agricultural traits. In this study, 29,357 potential SSRs were identified in 22,806 unigenes assembled from A. hypogaea transcript sequences. Of these unigenes, 1883 and 4103 were annotated and assigned in Kyoto Encyclopedia of Genes and Genomes Orthology and Eukaryotic Orthologous Groups databases, respectively. Among the SSR motifs, mono- (19,065; 64.94%) and trinucleotide (5033; 17.14%) repeats were the most common, and the three most dominant motifs were A/T (18,358; 62.54%), AG/CT (2804; 9.55%), and AAG/CTT (1396; 4.76%). Polymerase chain reaction (PCR) primer pairs were designed for 4340 novel SSR markers and 210 new SSRs were validated using 24 A. hypogaea varieties. Of the 210, 191 (91%) yielded PCR products, with 37 (18%) identifying polymorphisms. The 37 polymorphic SSR markers detected 146 alleles (2–10 alleles per locus), and the average polymorphic information content was 0.403 (with a range of 0.077 to 0.819). The new SSRs enrich the current marker resources for A. hypogaea and may also be useful for genetic diversity analysis, functional genomics research, and molecular breeding.
