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Genetic Diversity in Bamboos: Conservation and Improvement for Productivity Ajay Thakur, Santan Barthwal and H.S

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6 Genetic Diversity in Bamboos: Conservation and Improvement for Productivity Ajay Thakur, Santan Barthwal and H.S. Ginwal 1. Introduction Bamboos are interesting plants in their growth, morphogenesis, taxonomy, distribution, ecology, reproduction as well as diversity. Bamboos belong to the subfamily Bambusoideae of grass family, Poaceae. Woody bamboos mostly belong to Bambuseae tribe which is further divided into nine subtribes and 67 genera (Ramanayake et al., 2007). An estimated 1,400 bamboo species are distributed across the globe from 51oN latitude in Island of Sakhalin (Japan) to 47oS latitude in South Argentina. The bamboos can grow in an altitudinal range which extends from just above the sea level up to 4,000 m (Behari, 2006). The major species richness is found in Asia-Pacific region followed by South America, whereas the least number of species are found in Africa (Bystriakova et al., 2003). Bamboos can thrive in hot, humid rainforests to cold resilient forests. They can tolerate as well as grow in extreme low temperature of about - 20oC and precipitation ranging from 800 mm to 1,300 mm annual rainfall (Goyal et al., 2012). Asia alone is estimated to have more than 6.3 Mkm2 of bamboo forests, with most densities indicated from southern China to northeastern India and through Sumatra to Borneo. The maximum species richness (144 spp km-2) was estimated in forests of south China, including Hainan Island (Bystriakova et al., 2003). It is the fastest growing perennial and its morphogenesis includes functioning of intercalary meristem which supports rapid growth of internodes and their elongation to form the erect stem axis supported by considerable amount of lignin. Such magnificent growth habit shows its potential to suffice the demand of wood biomass despite that bamboos are still considered as poor man's timber. Traditionally, most commercially used bamboos are 38 species belonging to nine genera that comprise only a small portion of bamboo resources and those were 132 Ajay Thakur, Santan Barthwal and H.S. Ginwal explicitly narrowed down for genetic improvement studies (Williams and Rao, 1994; Rao et al., 1998). Genetic improvement of bamboos were discussed during late nineties and it was advocated to promote work on genetic analysis and conservation (Rao et al., 1998). Studies on genetic variation started in early twentieth century but halted for some time and again restarted during later part of that century. DNA based techniques made understanding of evolutionary trends in bamboos along with inter- and intra-specific relationships easy and now being used in population and conservation genetics. There is a need to understand genetic variation of woody bamboos on morphological, cytological and molecular basis vis-à-vis relationship between them. This chapter reviews the genetic diversity and improvement of bamboo species using classical as well as molecular genetics approach. 2. Bamboos: Genetic Variation and Evolution of Species 2.1.Phenotypic Variation Genetic diversity is the main building block for evolution and speciation. Bamboos are such a diverse group and provide many good examples to analyze and discuss the morphological and genetic concepts of species. A wide spectrum of variability is noticed within species of bamboos in natural distribution. Phenotypic variability exists with respect to flowering of bamboos, morphological traits like internodal length, culm wall thickness, sheath size and their cytology, variation in chromosome number, pollen grain size, fertility and germination. Variation also exists with respect to morphological and anatomical features. Kochhar et al. (1990) studies on populations of Bambusa pallida, B. tulda and Dendrocalamus hamiltonii and at West Siang (Arunachal Pradesh) and North Lakhimpur showed little interspecific and more intraspecific variation for seven clump management and five clump morphological traits in the base population. These characterization of traits paved way for improvement through selection of plus bamboo clumps from polymorphic populations based on individual traits. Spontaneous mutants with morphological variations were detected in colour, shape and structure in B. bambos, B. vulgaris, Guadua angustifolia, Oxytenanthera abyssinica and Phyllostachys edulis (Venkatesh, 1984). Genetic variations are recorded in certain species of bamboo most likely due to putative outcrossing, segregation and recombination. Inter- and intra- species variability in end-use linked chemical composition of five commercially important bamboo species, namely, B. balcooa, B. nutans, B. pallida, B. tulda and D. hamiltonii was analysed. High range of lignin content in B. nutans (25.64-29.46%) and that of holocelulose content in B. tulda (70.7-75.0 %) (Thakur et al., 2014). Genetic Diversity in Bamboos: Conservation and Improvement for Productivity 133 2.2.Genetic Variation DNA based molecular markers paved way for fast and reliable estimates of genetic diversity and distance. Considering complexities in taxonomic status of bamboo; mostly due to long flowering interval, initial studies have been focused on molecular phylogeny and taxonomy and a few were on intra specific diversity of bamboo. Molecular markers like random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR), simple sequence repeat (SSR), expression sequence tag (EST), chloroplast (cp) genome, single nucleotide polymorphic (SNP) markers, etc. are being used for phylogeny, inter- and intra-specific studies. Universally marker based techniques like AFLP, ISSR and cp genome are effective for phylogenetic studies, whereas RAPD and SSRs are co- dominant markers and have high rate of mutation, hence effective in studies related to genetic diversity. AFLP marker technique has been widely used to assess genetic diversity within and among the population of different bamboo species (Ghosh et al., 2011). Four genera of tropical bamboos: Bambusa, Dendrocalamus, Gigantochloa and Thyrsostachys are being reported to be differentiated by AFLP markers and with unique AFLPs for 13 out of 15 species (Loh et al., 2000). Bambusa (six species) is separated into two clusters, Gigantochloa (six species) has formed a discrete cluster diverging Bambusa clusters, while Thyrsostachys is less similar to the Bambusa clusters. Among Dendrocalamus, two species were reported to be different than D. brandisii, clustering within one of the Bambusa clusters. Interspecific diversity studies between nine species of tropical bamboos: Arundinaria hindsii, Bambusa atra, B. bambos, B. ventricosa, B. vulgaris 'Striata', D. asper, D. giganteus, D. longispathus and Gigantochloa atroviolacea using RAPD reveals that contrary to distinguished morphological dissimilarity between B. ventricosa and B. vulgaris, their genetic distance was only 0.143 (Ramanayake et al., 2007). Genetic distance between B. atra from B. vulgaris, B. ventricosa and B. bambos are greater as compared to G. atroviolacea. A. hindsii is most genetically distant from all other species and not related to any of them. A high level of genetic diversity was recorded in molecular analysis of random collections of industrially important reed bamboos (Ochlandra travancorica) using RAPD and AFLP marker technique. Microsatellite or SSR markers are valuable tool for genetic diversity analysis. SSR developed for cereal crops has been cross amplified for other bamboo species and successfully used for genetic diversity studies (Barkley et al., 2005; Dong et al., 2011; Zhang et al., 2011). Polymorphic EST-SSR markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified into 11 separate genera and 44 species (Barkley et al., 2005). The resulting dendrograms have two distinct clusters of main 134 Ajay Thakur, Santan Barthwal and H.S. Ginwal clades, which correspond to accessions into either clumping (sympodial) or running (monopodial) bamboos. Similarly, cross amplification of SSR markers of rice and sugarcane were successfully used for analysis of genetic diversity of 23 bamboo species (Sharma et al., 2008). In 20 accessions of D. hamiltonii, genetic diversity was 0.25. SSR markers were identified and characterized from B. bambos and tested for cross amplification in other 18 bamboo species (Nayak et al., 2003). Many novel microsatellite markers have also been developed in some bamboo species using method based on microsatellite enriched genomic library. Availability of draft genome sequence of P. heterocycla var. pubescens (Peng et al., 2013), opens another possibility to use its SSR markers in other bamboo species for assessment of genetic diversity and population genetics. 2.3.Molecular Phylogenomics Understanding of evolution of species is of prime importance for genetic studies and can be applied for improvement and conservation practices. Molecular phylogenomics based on whole cp genome can be used to resolve major relationships within and between subfamilies. Divergence of Bambusoideae from Poaceae is important to study because former is the only subfamily of Poaceae that contains woody members. Three subfamilies of Poaceae, i.e., Bambusoideae, Ehrhartoideae and Pooideae, formed the BEP clade, yet the internal relationships of this clade are controversial. Phylogeny construction of Poaceae from 24 complete chloroplast (cp) genomes including 21 grass species shows difficulty in resolving the diversification among three BEP clade, though it
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