Introduction
Jatropha curcas L. has been recognized as a major biodiesel crop (Fairless, Reference Fairless2007). It has a special feature as a renewable energy source due to its comparatively higher oil content than other non-edible oilseeds (Openshaw, Reference Openshaw2000). It is native to Mexico and Central America from where it has been taken to different tropical and subtropical regions of the world (Heller, Reference Heller1996; Pamidimarri and Reddy, Reference Pamidimarri and Reddy2014).
Availability of a genetically diverse germplasm is important for genetic improvement programmes. High phenotypic variability with respect to oil traits has been reported in Indian accessions of J. curcas (Kaushik et al., Reference Kaushik, Kumar, Kumar, Kaushik and Roy2007). However, most of the genetic diversity studies conducted using DNA-based markers have shown low genetic diversity within Indian accessions (Ranade et al., Reference Ranade, Srivastava, Rana, Srivastava and Tuli2008; Sujatha et al., Reference Sujatha, Reddy and Mahasi2008; Tatikonda et al., Reference Tatikonda, Wani, Kannan, Beerelli, Sreedevi, Hoisington, Devi and Varshney2009; Mastan et al., Reference Mastan, Pamidimarri, Rahman, Ghosh, Rathore, Ravi Prakash and Chikara2012).
Identification of a core collection is an important step towards management and utilization of genetic resources. The core collection, a subsample of the whole collection, typically comprises approximately 10% of all available accessions and is intended to provide a set of genetically diverse material (Brown, Reference Brown1989; Schoen and Brown, Reference Schoen and Brown1993). A number of studies have used amplified fragment length polymorphism (AFLP) markers for identification of core collections due to their high abundance and ease of genotyping (Jansen and van Hintum, Reference Jansen and van Hintum2007; Bamberg and del Rio, Reference Bamberg and del Rio2014).
In this study, AFLP markers were used for characterization of genetic diversity and identification of core accessions from an existing collection of J. curcas accessions collected solely based on geographical locations. The accessions of this core collection are conserved in TERI's Jatropha germplasm and can be made available for research purpose on request.
Experimental methods
A set of 192 accessions collected from India and five other countries were used (Tables S1 and S2, available online). AFLP genotyping was carried out using the standard AFLP protocol (Vos et al., Reference Vos, Hogers, Bleeker, Reijans, van de Lee, Hornes, Friters, Pot, Paleman, Kuiper and Zabeau1995). The amplification products were labelled with 32P and detected by autoradiography. Various marker attributes such as polymorphism information content (PIC) (Roldan-Ruiz et al., Reference Roldan-Ruiz, Dendauw, VanBockstaele, Depicker and Loose2000), marker index (MI) and resolving power (RP) (Prevost and Wilkinson, Reference Prevost and Wilkinson1999) were calculated. The binary matrix was used to estimate genetic similarity using Jaccard's coefficient. Clustering was performed based on UPGMA (Unweighted Pair Group Method of Arithmetic Averages) using only polymorphic bands. All the above-mentioned analyses were performed using the NTSys-PC software (version 2.20; Exeter software, New York, USA) (Rohlf, Reference Rohlf2000). The reliability and robustness of the dendrogram topology were analysed by bootstrap analysis (1000 re-samplings) using the DARwin software (version 5) (Perrier and Jacquemoud-Collet, Reference Perrier and Jacquemoud-Collet2006). Principal coordinate analysis (PCoA) and analysis of molecular variance were carried out using the software GenAlEx version 6.5 (Peakall and Smouse, Reference Peakall and Smouse2006). Core collections were identified based on AFLP data using PowerCore version 1.0 through heuristic search option (Kim et al., Reference Kim, Chung, Cho, Ma, Chandrabalan, Gwag, Kim, Cho and Park2007).
Discussion
A total of 319 bands were obtained using five primer combinations, out of which 109 (34.1%) were polymorphic (Table S4, available online). Primer combination E-AA × M-CTA displayed the highest values for PIC (0.16), RP (4.55) and MI (3.32), whereas the primer combination E-AG × M-CTA had the lowest values for these attributes. Pairwise Jaccard's similarity coefficient for accessions ranged from 0.25 (Jc428 (Mexico) vs. J204 (Tamil Nadu, India) to 1. A large number of accessions showed 100% similarity to other accessions indicating existence of duplicate accessions. While most of the duplicate accessions were found within and across the Indian states, several duplicate accessions across different countries were also found (Table S3, available online).
High genetic similarity has been reported in accessions from India, China, Singapore, Africa and Southern America (Ranade et al., Reference Ranade, Srivastava, Rana, Srivastava and Tuli2008; Sujatha et al., Reference Sujatha, Reddy and Mahasi2008; Sun et al., Reference Sun, Li, Li, Wu and Ge2008; Ambrosi et al., Reference Ambrosi, Galla, Purelli, Barbi, Fabbri, Lucretti, Sharbel and Barcaccia2010; Wang et al., Reference Wang, Liu, Yi, Gu, Sun, Li, Lo, Liu, Feng, Lin, Cao, Hong, Yin and Yue2011). Low genetic diversity in J. curcas germplasm seems to be a common problem in all countries where it has been introduced. This may be a result of founder effect, which occurs due to introduction of a population of highly related individuals (Wright, Reference Wright1931; Provine, Reference Provine2004).
Out of the three major clusters obtained, Cluster I included 144 accessions all of which were from India. Cluster II contained 35 accessions from Congo, Ethiopia, Nigeria, China and India, which may be indicative of germplasm flow between these countries. Cluster III included 13 Mexican accessions revealing their high divergence from other accessions. This is in agreement with a prevalent view of Mexico and Central America being the centre of origin of Jatropha (Ovando-Medina et al., Reference Ovando-Medina, Sanchez-Gutierrez, Adriano-Anaya, Espinosa-Garcia, Nunez-Farfan and Salvador-Figueroa2011; Pamidimarri and Reddy, Reference Pamidimarri and Reddy2014). PCoA also revealed similar grouping (Fig. 1 and Fig. S1, available online). Fifty-nine percent of the genetic variation was distributed among the clusters, while 41% of variation was within the clusters.
Dendrogram showing clustering of Jatropha curcas accessions using the UPGMA method. Cluster I: Indian accessions; Cluster II: African, Chinese and Indian accessions; Cluster III: Mexican accessions. The asterisk marks (*) against the accession IDs denote core accessions. Bootstrap values greater than 50 were considered significant and are shown in the figure.
A total of 16 (8.3% of the entire collection) core accessions were identified using the PowerCore program (Table 1). The core accessions harboured the entire allelic diversity of the germplasm collection. Six accessions were selected each from clusters I (India) and III (Mexico), whereas four accessions were identified from cluster II (Congo, Ethiopia and India). Among the eight Indian accessions, four accessions were from southern India, two from northern India and one accession each from west and southwest India. The Indian core accessions thus represented seven states covering almost 90% of latitudinal span of the country (Table S1, available online). One of these accessions, Jc440, collected from northwest India (Rajasthan) was highly distinct with triangular fruits and extremely short internodes leading to a dwarf phenotype, which is highly desirable for high-density plantation and manual harvesting. Introduction of dwarfing genes such as Rht in wheat and sd-1 in rice has a well-known history of success in increasing productivity of these crops during 1960s leading to green revolution (Spielmeyer et al., Reference Spielmeyer, Ellis and Chandler2002; Borojevic and Borojevic, Reference Borojevic and Borojevic2005). The current genetic and phenotypic information would enhance the optimal utilization of these accessions in future breeding programmes. It would be logical to pyramid together the various desirable traits such as dwarf plant height, large fruit size, etc., to develop varieties with increased seed yield. The core accessions could also be used as a reference for germplasm acquisition/introduction initiatives in India. Overall, the core accessions would be highly useful for future genetic improvement of Jatropha.
Jatropha curcas core accessions identified using AFLP data
Supplementary material
To view supplementary material for this article, please visit http://dx.doi.org/10.1017/S1479262115000088
Acknowledgements
This work was graciously funded by the Department of Biotechnology, Government of India. The authors acknowledge all the collaborating institutes of the Jatropha Micro Mission Program for sharing the leaf material of J. curcas accessions. Pratima Sinha is thankful to the Ministry of New and Renewable Energy (MNRE), Government of India, for providing fellowship for this work. The authors are thankful to Dr R.K. Pachauri, Director General, TERI, for his kind support.
