Phylogenetic Analysis of Different Ploidy Saccharum Spontaneum Based on Rdna-ITS Sequences

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Phylogenetic Analysis of Different Ploidy Saccharum Spontaneum Based on Rdna-ITS Sequences RESEARCH ARTICLE Phylogenetic Analysis of Different Ploidy Saccharum spontaneum Based on rDNA-ITS Sequences Xinlong Liu1,2, Xujuan Li2, Hongbo Liu2, Chaohua Xu2, Xiuqin Lin2, Chunjia Li2, Zuhu Deng1* 1 Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China, 2 Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China * [email protected] Abstract Saccharum spontaneum L. is a crucial wild parent of modern sugarcane cultivars whose ploidy OPEN ACCESS clones have been utilized successfully in improving the stress resistance and yield related Citation: Liu X, Li X, Liu H, Xu C, Lin X, Li C, et al. traits of sugarcane cultivars. To establish knowledge regarding the genetic variances and evo- (2016) Phylogenetic Analysis of Different Ploidy lutional relationships of ploidy clones of Saccharum spontaneum collected in China, the rDNA- Saccharum spontaneum Based on rDNA-ITS ITS sequences of 62 ploidy clones including octaploid clones (2n = 64), nonaploid clones (2n Sequences. PLoS ONE 11(3): e0151524. = 72), decaploid clones (2n = 80), and dodecaploid clones (2n = 96), were obtained and ana- doi:10.1371/journal.pone.0151524 lyzed. The rDNA-ITS sequences of four species from Saccharum and Sorghum bicolor Editor: Tzen-Yuh Chiang, National Cheng-Kung selected as controls. The results showed that decaploid clones (2n = 80) possess the most University, TAIWAN abundant variances with 58 variable sites and 20 parsim-informative sites in ITS sequences, Received: October 8, 2015 which were then followed by octaploid clones with 43 variable sites and 17 parsim-informative Accepted: February 28, 2016 sites. In haplotype diversity, all four population exhibited high diversity, especially nonaploid Published: March 17, 2016 and decaploid populations. By comparing the genetic distances among four ploidy popula- Copyright: © 2016 Liu et al. This is an open access tions, the dodecaploid population exhibited the closest relationship with the nonaploid popula- article distributed under the terms of the Creative tion, and then the relationship strength decreased successively for the decaploid population Commons Attribution License, which permits and then for the octaploid population. Population differentiation analysis showed that the phe- unrestricted use, distribution, and reproduction in any nomena of population differentiation were not found among different ploidy populations, and medium, provided the original author and source are credited. low coefficient of gene differentiation(Gst) and high gene flow(Nm) occur among these popula- tions possessing close genetic relationship. These results mentioned above will contribute to Data Availability Statement: All sequence data have been uploaded to GenBank, their acession No. the understanding of the evolution of different ploidy populations of Saccharum spontaneum are KJ934283, KJ934287, KJ934293, KJ934276, and provide vital knowledge for their utilization in sugarcane breeding and innovation. KJ934285, KJ934288, KJ934274, KJ934280, KJ934291, KJ934290, KJ934275, KJ934294, KJ934273, KJ934284, KJ934278, KJ934281, KJ934289, KJ934279, KJ934292, KJ934282, KJ934277, KJ934286, KJ934297, KJ934296, KJ934298, KJ934300, KJ934299, KJ934295, Introduction KJ934301, KJ934334, KJ934333, KJ934332, KJ934303, KJ934304, KJ934307, KJ934306, Saccharum spontaneum L. is a crucial wild parent for modern sugarcane cultivars that can KJ934312, KJ934311, KJ934338, KJ934337, improve cultivars with regards to tolerances to abiotic or biotic stress and yield related traits. More KJ934302, KJ934340, KJ934313, KJ934343, notably it has the widest ecogeographical distribution among Saccharum spp. and different clones PLOS ONE | DOI:10.1371/journal.pone.0151524 March 17, 2016 1/12 Phylogenetic Analysis of Different Ploidy Saccharum spontaneum Based on rDNA-ITS Sequences KJ934341, KJ934346, KJ934324, KJ934325, show wide morphological variation [1]. Clones vary from short bushy types with reduced leaves KJ934326, KJ934347, KJ934342, KJ934316, to midrib and practically no formation to tall, erect, broad-leaved forms with long internodes [2]. KJ934358, KJ934353, KJ934354, KJ934355, In China, the plant is distributed mainly in the central, southern, and southwest parts [3]. KJ934356, KJ934357, KJ934359, KJ934360, KJ934361, KJ934352. S. spontaneum also belongs to the complex polyploid plants like sugarcane, whose chromo- some number has been reported to range from 2n = 40 to 128 with basic number of chromosome Funding: This work was supported by the Yunnan x = 8, and five types of chromosome number (2n = 64, 80, 96, 112, and 128) appear to be distrib- Natural Science Foundation (2011FB120) funder – name: Xinlong Liu, conceived and designed the uted highly frequency [4 6]. Studies using GISH and FISH techniques dissected the chromosome experiments, the National Natural Science composition of model sugarcane cultivars revealed that approximately 10–20% of total chromo- Foundation of China (31360359) funder name: somes of cultivars come from S. spontaneum and that about 10% of these occurred in the inter- Xinlong Liu, conceived and designed the specific exchange between S. spontaneum and S. officinarum [7–9]. These studies have confirmed experiments; the Earmarked Fund for the Modern that S. spontaneum has become an important component of modern sugarcane cultivars. Agriculture Technology of China (CARS-20-1-5), funder name: Zuhu Deng, conceived and designed During the past several years, research communities around the world have mainly focused the experiments; Candidates of the Young and Middle their studies on the genetic diversity of clones of S. spontaneum collected from different areas. Aged Academic Leaders of Yunnan Province This studies have proved that S. spontaneum possess very rich genetic variances in phenotypic (2014HB038), funder name: Xinlong Liu, conceived and molecular level traits [10–15]. In addition, because S. spontaneum is easy to cross with S. and designed the experiments. officinarum & sugarcane cultivars and their offspring exhibit good performance in stress resis- Competing Interests: The authors have declared tance, adaptability, and ratoon capability S. spontaneum is regarded as one of the most valuable that no competing interests exist. wild specie for exploring sugarcane breeding [1]. When reviewing the history of sugarcane breeding, it is unfortunate that only limited euploid clones of S. spontaneum, including Glagah (2n = 112), Indian (2n = 64), and Yacheng (2n = 64, 80), have been utilized successfully in sugarcane breeding and were used to make series of elite parents such as the POJ series, the Co series and the Yacheng series. To date, these parents still play a critical role in breeding [1, 16]. Since the 1970s, the collecting work of S. spontaneum has been carried out in China. At present about 700 clones, which were collected from Yunnan, Guangxi, Guangdong, Fujian, Sichuan, and Hainan, were conserved in the China National Nursery of Sugarcane Germplasm Resources (CNNSGR) in Kaiyuan, Yunnan province. By identifying the chromosome number of 247 clones conserved in CNNSGR, Cai et al. [17] found 11 chromosome types that are 2n = 60, 64, 70, 72, 74, 78, 80, 92, 96, 104, 108 and 4 which were euploid types (2n = 64, 72, 80, 96) make up a high percentage in all identified clones. Currently, the genetic background and evolutionary relationships for these euploid clones still remain unclear, which has limited their utilization in sugarcane breeding. At present, some sequences such as rDNA-ITS, rbcl, apha-tubulin, rpl16 and rpoC2 have been using in the genetic relationship analysis of these species belong to Saccharum L. and other related genus as Miscanthus Anderss., Erianthus Michaux and Narenga Bor. [18–23]. These pre- vious studies demonstrated that these sequences except rDNA-ITS are very conserved among different species, which suit for evolutionary analysis of different genus. For rDNA-ITS, the characters of rich variances, rapid evolutionary rate and easy PCR amplification make it a very important marker used in the evolutionary analysis of "sugarcane complex", and it also is often used to evaluate evolutionary relationships at the subspecies level [24]. In view of this, 62 ploidy clones belonging to 4 euploid types of S. spontaneum, were evaluated in this study for genetic variances and phylogenetic relationships via the rDNA-ITS sequences. The results will provide informative knowledge for utilization in sugarcane breeding and innovation. Materials and Methods Ethics Statement S. spontaneum is not considered an endangered species, collecting is allowed in field environ- ment. These S. spontaneum clones in this study were collected in recent decades by Yunnan PLOS ONE | DOI:10.1371/journal.pone.0151524 March 17, 2016 2/12 Phylogenetic Analysis of Different Ploidy Saccharum spontaneum Based on rDNA-ITS Sequences Sugarcane Research Institute (YSRI). At present, these clones were conserved in the CNNSGR (China National Nursery of Sugarcane Germplasm Resources), which was built by China's Ministry of Agriculture in Kaiyuan city, Yunan province in 1995. The YSRI was entrusted with managing the routine works of CNNSGR. We were assigned to responsible for management, evaluation of these resources by YSRI. Finally, we confirm that no specific permits were required for the present studies. Plant materials A total of 62 different ploidy clones of S. spontaneum
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