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Genetic diversity of Jatropha curcas collections from different islands in Indonesia

Published online by Cambridge University Press:  05 March 2018

Tantri Dyah Ayu Anggraeni ,
Dani Satyawan ,
Yang Jae Kang ,
Jungmin Ha ,
Moon Young Kim ,
Annapurna Chitikineni ,
Rajeev K. Varshney  and
Suk-Ha Lee
Tantri Dyah Ayu Anggraeni
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Indonesian Sweetener and Fiber Crops Research Institute, IAARD, Malang 65100, Indonesia
Dani Satyawan
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Indonesian Center for Agricultural Biotechnology and Genetic Resources and Development, IAARD, Bogor 16111, Indonesia
Yang Jae Kang
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
Jungmin Ha
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
Moon Young Kim
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
Annapurna Chitikineni
Affiliation:
Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Andhra Pradesh, India
Rajeev K. Varshney
Affiliation:
Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Andhra Pradesh, India
Suk-Ha Lee*
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
*
*Corresponding author. E-mail: sukhalee@snu.ac.kr
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Abstract

Jatropha curcas L. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding of J. curcas germplasm is important for designing breeding strategies. This study was performed to investigate the genetic diversity and population structure of Indonesian J. curcas populations from six different islands. To construct a reference, we de novo assembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from Thai J. curcas variety Chai Nat. Genetic diversity analysis among 52 Indonesian J. curcas accessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. Using J. integerrima as an outgroup, 13,916 SNPs were detected. Among J. curcas accessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among Indonesian J. curcas populations, representing low genetic diversity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of diverse J. curcas germplasms is necessary for the improvement of the genetic variation in the Indonesian collections.

Keywords

genetic diversitygenotyping-by-sequencingIndonesiaislandsJatropha curcasmigratory rout
Type
Research Article
Information
Plant Genetic Resources , Volume 16 , Issue 4 , August 2018 , pp. 334 - 342
Copyright
Copyright © NIAB 2018 

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