Junjie Cui1, Jiazhu Peng2, Jiaowen Cheng3, Kailin Hu4. 1. Department of Horticulture, Foshan University, Foshan, Guangdong, 528225, People's Republic of China. 2. Guangzhou Academy of Agricultural Sciences, Guangzhou, Guangdong, 510335, People's Republic of China. 3. College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China. 4. College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China. hukailin@scau.edu.cn.
Abstract
BACKGROUND: The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. RESULTS: Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines '47-2-1-1-3' and '04-17,' indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 '47-2-1-1-3' × '04-17' F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. CONCLUSIONS: This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.
BACKGROUND: The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. RESULTS: Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines '47-2-1-1-3' and '04-17,' indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 '47-2-1-1-3' × '04-17' F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. CONCLUSIONS: This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.
Authors: Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo Journal: Genome Res Date: 2010-07-19 Impact factor: 9.043
Authors: Ryan E Mills; Christopher T Luttig; Christine E Larkins; Adam Beauchamp; Circe Tsui; W Stephen Pittard; Scott E Devine Journal: Genome Res Date: 2006-08-10 Impact factor: 9.043