Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species

doi:10.1016/j.pld.2018.11.005

Abstract

Abstract: Date palm (Phoenix dactylifera), one of the most ancient crops, is grown commercially in>30 countries. Using whole plastome assemblies, phylogenetic analyses revealed that cultivated date palm accessions share the same clade with Phoenix sylvestris, Phoenix pusilla and Phoenix acaulis, which are native to the Indian subcontinent, and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia. Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci. Extensive genetic diversity was observed, with many accessions heterozygous for most markers in this clonally propagated crop. The average number of alleles per locus (42.1), expected heterozygosity (0.8), observed heterozygosity (0.47) and fixation indices (F_ST=0.42) demonstrated substantial genetic diversity and population structure. Iraqi accessions were found to have the richest allelic diversity, and the most private alleles. The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups, one group with predominantly African accessions and another predominantly Asian. Some germplasm, especially from Tunisia and Iraq, deviated from this generalization. Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures, with gene flow between Asian and African groups. Indian and Pakistani date palms were found to be most closely related to North African germplasm.

Key words: Date palm improvement, Germplasm dissemination, Plastome, Simple sequence repeats

Srinivasa R. Chaluvadi, Porter Young, Kentrez Thompson, Bochra Amina Bahri, Bhavesh Gajera, Subhash Narayanan, Robert Krueger, Jeffrey L. Bennetzen. Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species[J]. Plant Diversity, 2019, 41(05): 330-339.

Figures/Tables 4

References 32

1	Aleric KM, Kirkman LK (2005). Growth and photosynthetic responses of the federally endangered shrub, Lindera melissifolia (Lauraceae), to varied light environments.American Journal of Botany, 92, 682-689.
2	Baker NR (2008). Chlorophyll fluorescence: A probe of photosynthesis in vivo.Annual Review of Plant Biology, 59, 89-113.
3	Chen DR (2008). Rhododendron simsii., Rh. pulchrum, Rh. mucronatum, Rh. indicum.Guangdong Landscape Architecture, 30, 77-78.(in Chinese with English abstract) [陈定如 (2008). 映山红、锦绣杜鹃、白花杜鹃、皋月杜鹃. 广东园林, 30(2), 77-78.]
4	Chen J, Mao ZJ, Ma LX, Xia YY (2008). Response of photosynthetic capacity and chlorophyll fluorescence in Quercus mongolica and Tilia amurensis seedlings after light intensity transfer.Bulletin of Botanical Research, 28, 471-476.(in Chinese with English abstract) [陈婕, 毛子军, 马立祥, 夏莹莹 (2008). 蒙古栎和紫椴幼苗对光环境转变的光合作用响应. 植物研究, 28, 471-476.]
5	Demmig-Adams B (1998). Survey of thermal energy dissipation and pigment composition in sun and shade leaves.Plant and Cell Physiology, 39, 474-482.
6	Demmig-Adams B, Adams III WW (1992). Photoprotection and other responses of plants to high light stress.Annual Review of Plant Physiology and Plant Molecular Biology, 43, 599-626.
7	Du N, Zhang XR, Wang W, Chen H, Tian XF, Wang RQ, Guo WH (2011). Foliar phenotypic plasticity of a warm- temperate shrub, Vitex negundo var. heterophylla, to different light environments in the field.Acta Ecologica Sinica, 31, 6049-6059.(in Chinese with English abstract) [杜宁, 张秀茹, 王炜, 陈华, 谭向峰, 王仁卿, 郭卫华 (2011). 荆条叶性状对野外不同光环境的表型可塑性. 生态学报, 31, 6049-6059.]
8	Duan BL, Lü YW, Yin CY, Li CY (2005). Morphological and physiological plasticity of woody plant in response to high light and low light.Chinese Journal of Applied & Environmental Biology, 11, 238-245.(in Chinese with English abstract) [段宝利, 吕艳伟, 尹春英, 李春阳 (2005). 高光和低光下木本植物形态和生理可塑性响应. 应用与环境生物学报, 11, 238-245.]
9	Feng YL, Cao KF, Feng ZL, Ma L (2002). Acclimation of lamina mass per unit area, photosynthetic characteristics and dark respiration to growth light regimes in four tropical rainforest species.Acta Ecologica Sinica, 22, 901-910.(in Chinese with English abstract) [冯玉龙, 曹坤芳, 冯志立, 马玲 (2002). 四种热带雨林树种幼苗比叶重, 光合特性和暗呼吸对生长光环境的适应. 生态学报, 22, 901-910.]
10	Guan M, Jin ZX, Wang Q, Li YL, Zuo W (2014). Response of photosynthesis traits of dominant plant species to different light regimes in the secondary forest in the area of Qiandao Lake, Zhejiang, China.Chinese Journal of Applied Ecology, 25, 1615-1622.(in Chinese with English abstract) [管铭, 金则新, 王强, 李月灵, 左威 (2014). 千岛湖次生林优势种植物光合特性对不同光环境的响应. 应用生态学报, 25, 1615-1622.]
11	Heraud P, Beardall J (2000). Changes in chlorophyll fluorescence during exposure of Dunaliella tertiolecta to UV radiation indicate a dynamic interaction between damage and repair processes.Photosynthesis Research, 63, 123-134.
12	Hu QP, Guo ZH, Li CY, Ma LY (2008). Leaf morphology and photosynthetic characteristics of seedlings of a deciduous and an evergreen broad-leaved species under different light regimes in subtropical forests.Acta Ecologica Sinica, 28, 3262-3270.(in Chinese with English abstract) [胡启鹏, 郭志华, 李春燕, 马履一 (2008). 不同光环境下亚热带常绿阔叶树种和落叶阔叶树种幼苗的叶形态和光合生理特征. 生态学报, 28, 3262-3270.]
13	Hu WH, Zhang SS, Yan XH, Xiao YA (2014). Effects of natural sunlight on photoinhibition and photoprotection mechanisms in Rhododendron molle leaves from long term shading to sunny days. Journal of Jinggangshan University (Natural Science), 35(5), 42-46.(in Chinese with English abstract) [胡文海, 张斯斯, 闫小红, 肖宜安 (2014). 长期遮荫后全光照对羊踯躅叶片光抑制及光保护机制的影响. 井冈山大学学报(自然科学版),35(5), 42-46.]
14	Huang W, Zhang SB, Cao KF (2010). Stimulation of cyclic electron flow during recovery after chilling-induced photoinhibition of PSII.Plant and Cell Physiology, 51, 1922-1928.
15	Kramer DM, Johnson G, Kiirats O, Edwards GE (2004). New fluorescence parameters for the determination of QA redox state and excitation energy fluxes.Photosynthesis Research, 79, 209-218.
16	Li W, Zhang YL, Hu YY, Yang MS, Wu J, Zhang WF (2012). Research on the photoprotection and photosynthesis characteristics of young cotton leaves under field conditions.Chinese Journal of Plant Ecology, 36, 662-670.(in Chinese with English abstract) [李维, 张亚黎, 胡渊渊, 杨美森, 吴洁, 张旺锋 (2012). 田间条件下棉花幼叶光合特性及光保护机制. 植物生态学报, 36, 662-670.]
17	Li ZZ, Liu DH, Zhao SW, Jiang CD, Shi L (2014). Mechanisms of photoinhibition induced by high light in Hosta grown outdoors.Chinese Journal of Plant Ecology, 38, 720-728.(in Chinese with English abstract) [李志真, 刘东焕, 赵世伟, 姜闯道, 石雷 (2014). 环境强光诱导玉簪叶片光抑制的机制. 植物生态学报, 38, 720-728.]
18	Miyake C, Miyata M, Shinzaki Y, Tomizawa KI (2005). CO2 response of cyclic electron flow around PSI (CEF-PSI) in tobacco leaves-relative electron fluxes through PSI and PSII determine the magnitude of non-photochemical quenching (NPQ) of Chl fluorescence.Plant and Cell Physiology, 46, 629-637.
19	Murchie EH, Horton P (1998). Contrasting patterns of photosynthetic acclimation to the light environment are dependent on the differential expression of the responses to altered irradiance and spectral quality.Plant, Cell & Environment, 21, 139-148.
20	Nikiforou C, Nikolopoulos D, Manetas Y (2011). The winter- red-leaf syndrome in Pistacia lentiscus: Evidence that the anthocyanic phenotype suffers from nitrogen deficiency, low carboxylation efficiency and high risk of photoinhibition.Journal of Plant Physiology, 168, 2184-2187.
21	Qi X, Cao KF, Feng YL (2004). Photosynthetic acclimation to different growth light environments in seedlings of three tropical rainforest Syzygium species.Acta Phytoecologica Sinica, 28, 31-38.(in Chinese with English abstract) [齐欣, 曹坤芳, 冯玉龙 (2004). 热带雨林蒲桃属3个树种的幼苗光合作用对生长光强的适应. 植物生态学报, 28, 31-38.]
22	Ralph PJ, Gademann R (2005). Rapid light curves: A powerful tool to assess photosynthetic activity.Aquatic Botany, 82, 222-237.
23	Shang B (2000). Rhobdendron hybridn’s ecological features and cultivated technigues. Journal of Fuyang Teachers College (Natural Science), 17(3), 26-28.(in Chinese with English abstract) [尚冰 (2000). 比利时杜鹃的生态特性与栽培技术. 阜阳师范学院学报(自然科学版), 17(3), 26-28.]
24	Tang H, Wang ML, Wei JQ, Wei X, Jiang YS, Chai SF (2010). Comparison on leaf morphological and photosynthetic characteristics of Illicicum difengpi K. I. B. et K. I. M grown in full light and under canopy.Plant Physiology Communications, 46, 949-952.(in Chinese with English abstract) [唐辉, 王满莲, 韦记青, 韦霄, 蒋运生, 柴胜丰 (2010). 林下与全光下地枫皮叶片形态和光合特性的比较. 植物生理学通讯, 46, 949-952.]
25	Urban O, Košvancová M, Marek MV, Lichtenthaler HK (2007). Induction of photosynthesis and importance of limitations during the induction phase in sun and shade leaves of five ecologically contrasting tree species from the temperate zone.Tree Physiology, 27, 1207-1215.
26	Wang BY, Ma HJ, Su TW, Liu T, Wang Q (2012). Physiological response and acclimation to changes in light regimes in two tropical rainforest species.Plant Physiology Journal, 48, 232-240.(in Chinese with English abstract) [王博轶, 马洪军, 苏腾伟, 刘涛, 王齐 (2012). 两种热带雨林树苗对环境光强变化的生理响应和适应机制. 植物生理学报, 48, 232-240.]
27	Wang ML, Wei X, Tang H, Liang HL, Zhou R (2015). Effects of light intensity on growth and photosynthesis of three karst plant seedlings.Chinese Journal of Ecology, 34, 604-610.(in Chinese with English abstract) [王满莲, 韦霄, 唐辉, 梁惠凌, 邹蓉 (2015). 光强对三种喀斯特植物幼苗生长和光合特性的影响. 生态学杂志, 34, 604-610.]
28	Way DA, Pearcy RW (2012). Sunflecks in trees and forests: From photosynthetic physiology to global change biology.Tree Physiology, 32, 1066-1081.
29	Wyka T, Robakowski P, Zytkowiak R (2007). Acclimation of leaves to contrasting irradiance in juvenile trees differing in shade tolerance.Tree Physiology, 27, 1293-1306.
30	Xiang F, Zhou Q, Tian XR, Chen GX, Xiao Y (2014). Leaf morphology and PS II chlorophyll fluorescence parameters in leaves of Sinosenecio jishouensis in different habitats.Acta Ecologica Sinica, 34, 337-344.(in Chinese with English abstract) [向芬, 周强, 田向荣, 陈功锡, 肖艳 (2014). 不同生境吉首蒲儿根叶片形态和叶绿素荧光特征的比较. 生态学报, 34, 337-344.]
31	Xue W, Li XY, Zhu JT, Lin LS, Wang YJ (2011). Effects of shading on leaf morphology and response characteristics of photosynthesis in Alhagi sparsifolia.Chinese Journal of Plant Ecology, 35, 82-90.(in Chinese with English abstract) [薛伟, 李向义, 朱军涛, 林丽莎, 王迎菊 (2011). 遮阴对疏叶骆驼刺叶形态和光合参数的影响. 植物生态学报, 35, 82-90.]
32	Ye ZP, Robakowski P, Suggett DJ (2013). A mechanistic model for the light response of photosynthetic electron transport rate based on light harvesting properties of photosynthetic pigment molecules.Planta, 237, 837-847.

参数 Parameter	比利时杜鹃 R. hybrida		杜鹃 R. simsii
参数 Parameter	遮阴 Shade	全光照 Sun	遮阴 Shade	全光照 Sun
F_v/F_m	0.793 ± 0.004^a	0.494 ± 0.029^b	0.817 ± 0.002^a	0.780 ± 0.002^b
α	0.392 ± 0.013^a	0.238 ± 0.018^b	0.333 ± 0.003^a	0.327 ± 0.007^a
J_max (μmol·m^-2·s^-1)	64.9 ± 6.8^a	37.8 ± 5.3^b	63.1 ± 8.3^a	74.9 ± 4.4^a
PAR_sat (μmol·m^-2·s^-1)	808.8 ± 37.0^a	818.4 ± 21.2^a	849.4 ± 24.3^b	943.2 ± 17.2^a

参数 Parameter	比利时杜鹃 R. hybrida		杜鹃 R. simsii
参数 Parameter	遮阴 Shade	全光照 Sun	遮阴 Shade	全光照 Sun
F_v/F_m	0.793 ± 0.004^a	0.494 ± 0.029^b	0.817 ± 0.002^a	0.780 ± 0.002^b
α	0.392 ± 0.013^a	0.238 ± 0.018^b	0.333 ± 0.003^a	0.327 ± 0.007^a
J_max (μmol·m^-2·s^-1)	64.9 ± 6.8^a	37.8 ± 5.3^b	63.1 ± 8.3^a	74.9 ± 4.4^a
PAR_sat (μmol·m^-2·s^-1)	808.8 ± 37.0^a	818.4 ± 21.2^a	849.4 ± 24.3^b	943.2 ± 17.2^a

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