Tree Genetics & Genomes

, 13:75 | Cite as

Genetic diversity of Southeastern Nigerien date palms reveals a secondary structure within Western populations

  • Oumarou Zango
  • Emira Cherif
  • Nathalie Chabrillange
  • Salwa Zehdi-Azouzi
  • Muriel Gros-Balthazard
  • Summar Abbas Naqvi
  • Alain Lemansour
  • Hervé Rey
  • Yacoubou Bakasso
  • Frédérique Aberlenc
Original Article
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Part of the following topical collections:
  1. Population structure

Abstract

Date palm (Phoenix dactylifera L.) is mainly cultivated for its edible fruit and is of great socio-economic importance for the populations of arid zones. Analysis of the date palm genetic diversity in the Old World had revealed a strong genetic structure with the existence of two gene pools, one Eastern comprising Asia and Djibouti, and one Western, consisting of North African accessions. So far, mainly date palm populations from countries within the Maghreb and the Middle East were characterized, but no information from the Sahel was included. Here, we present the genetic diversity of date palms from Southeastern Niger. The DNA of 113 date palm accessions were analyzed and compared with a database containing the genetic information of 248 accessions from the Old World. The diversity generated from microsatellite markers was compared to that of the same loci of both the Eastern and Western genetic pools. Our results show that date palms from Southeastern Niger constitute a unique group with a high level of genetic diversity. Moreover, even though this group is included in the Western genetic pool, it shows a specific originality which differentiates it from other Western populations. It also shows one of the lowest admixture levels of the Western pool. Global analysis showed a secondary genetic structure within the Western pool highlighting a new genetic group located in Southeastern Niger that distinguishes itself from the North African group.

Keywords

Date palm Genetic diversity Microsatellite markers Sahel Southeast Niger 

Introduction

Cultivated for over 6000 years mainly for its fruit (Terral et al. 2012; Tengberg 2012), the date palm is of great socio-economic importance in the Arabic Peninsula, North Africa, and Middle East (Bouguedoura 1979; Chao and Krueger 2007; Zango et al. 2013). Introduced in several areas of the world, including Asia, Spain, Australia, and the USA, it is also present in the Sahel, particularly in Niger, Mali, and Chad (Munier 1973; Barrow 1998).

In Niger, the date palm is cultivated in two main regions: in a traditional growing area in the Sahara and in a marginal cultivation area in the Sahelian part in the Southeast of the country. Traditional cultivation extends from the Aïr Mount to the Ingal Valley in the North and from the Djado Plateau to Kawar and Agram in the Northeast (Fig. 1a). The Djado and Kawar palm groves are natural stands mentioned for the first time in 1154 by the Arab geographer Idrisi and quoted by Munier (1963). The palm groves of Air and Ingal would originate from local seeds from Djado and Kawar or imported from Medina (Saudi Arabia) and would date from the sixteenth century (Munier 1963). However, the Sahel though is considered as a marginal area for date palm cultivation because of sustained rainfall and days of insufficient high temperature due to cloudiness during late fruit development, both influencing and altering fruit maturation. In this area, date palms would originate from seeds from Aïr, Djado, or Fezzan in Libya and would date from the years 1917 to 1918 (Munier 1963; Lenormand 1984). These groves are located in the Southeast of the country, specifically in Damagaran (the Zinder region) and Manga (the Diffa region) where they are grown in oasis basins and lowlands (Jahiel 1996; Zango et al. 2016). According to Lenormand (1984), date palms were first introduced in Damagaram and gradually moved further East to the Manga region from 1924.
Fig. 1

a Main date palm groves in Niger. b Southeast Niger date palm groves in Mirriah, Magariah, D. Takaya, Goure, and Goudoumaria departments

In the traditional date palm cultivation area (the Arabic Peninsula, North Africa, and the Middle East), the date palm biological cycle is characterized by a single annual flowering season. In the Sahel however, it presents a double flowering, which is peculiar in this area (Jahiel 1996; Zango et al. 2016). The first flowering covers over 45% of the date palm production and occurs from September to March (dry season). The second flowering occurs in all the palm trees and takes place from February to July during the rainy season (Zango et al. 2016). Date production during the second season is higher than that of during the first (Zango et al. 2016), but fruits are of poorer quality and conservation, because of the rainfall in June. Date palm cultivation is nonetheless widely recognized as an important activity to ensure food security in the Sahel in general and in Southeast Niger in particular (Munier 1973; Jahiel 1998; Zango et al. 2016) because it is strongly affected by aridity and ecosystem alteration (Ozer et al. 2010).

Advanced knowledge on date palm genetic resources in the Old World describes two distinct date palm genetic pools related to geographic distribution (Gros-Balthazard et al. 2013; Pintaud et al. 2013; Hazzouri et al. 2015; Zehdi-Azouzi et al. 2015). The Eastern pool covers Djibouti, Iraq, the United Arab Emirates, Oman, and Pakistan and the Western pool ranges from North Africa (Tunisia, Morocco, Algeria, Mauritania, Libya, Sudan, and Egypt) to Spain. Whereas, knowledge on genetic resources in Libya (Racchi et al. 2014), Tunisia (Zehdi-Azouzi et al. 2012; Zehdi-Azouzi et al. 2016), Algeria (Bennaceur et al. 1991), Morocco (Bodian et al. 2014), Mauritania (Bodian et al. 2012), Nigeria (Yusuf et al. 2015), and Sudan (Elshibli and Korpelainen 2008) is well advanced; the date palm germplasm in the Sahel is still unknown.

In the present study, we used three kinds of SSR markers (nuclear, chloroplast, and “Y” linked) to characterize the date palm genetic structure in Southeast Niger. The Nigerien date palm genetic diversity was also compared to the world genetic diversity in order to (i) identify the genetic pool to which it belongs and (ii) learn more about its origin.

Materials and methods

Plant material

The plant material was collected in five Southeastern Nigerien subgroups: three subgroups in the region of Damagaram: Damagaram Takaya (D. Takaya), Magariah, and Mirriah and two subgroups in the Manga region: Goure and Goudoumaria (Fig. 1b). A sampling of 113 date palms (31 males and 82 females) was collected from 19 oasis basins (Fig. 1). For each date palm, a sample of a leaflet was collected from the heart of the crown and stored with silica gel.

The genetic diversity of Nigerien date palms was compared to that of the Old World with 248 samples from Egypt (19), Libya (7), Mauritania (5), Morocco (16), Sudan (4), Tunisia (85), Iraq (14), Oman (27), Pakistan (51), and the United Arab Emirates (20) as described by Zehdi-Azouzi et al. (2015).

DNA preparation, amplification, and genotyping

Leaf samples were freeze-dried for 72 h with an Alpha1-4LD Plus lyophilizer (Fisher Scientific, Illkirch, France) and ground with a Tissue Lyser System (Qiagen SA, Courtabœuf, France). DNA extraction was carried out using the Dneasy plant mini kit (Qiagen SA, Courtabœuf, France) according to the manufacturer’s instructions.

In this study, 18 SSR loci (SSR details in Table 1, SSR references in Table S1) were amplified including dinucleotide repeats (Billotte et al. 2004; Ludeña et al. 2011) as well as tri/hexanucleotide repeats (Aberlenc-Bertossi et al. 2014; Zehdi-Azouzi et al. 2015). The plastid decanucleotide minisatellite (Table S1) identified in the intergenic spacer psbZ-trnfM (Henderson et al. 2006) was also amplified to identify the Western and Eastern chlorotypes as defined by Pintaud et al. (2010), within the sampling. Furthermore, three sex-linked loci (mPdIRDP50, mPdIRDP52, and mPdIRDP80) (Cherif et al. 2013) were used to identify the Western and Eastern Y haplotypes as defined by Cherif et al. (2013) (Table S1).
Table 1

Diversity generated by the microsatellite markers (markers referencea)

Marker

Na

Ng

Maf

Pic

He

Ho

Fis

mPdIRD013

2

2

0.991

0.017

0.022

0.023

−0.036

mPdIRD031

3

4

0.876

0.207

0.220

0.228

−0.037

mPdIRD033

3

6

0.788

0.316

0.344

0.328

0.049*

mPdIRD040

6

10

0.655

0.470

0.510

0.511

−0.003

mPdCIR010

10

25

0.323

0.737

0.729

0.642

0.119***

mPdCIR015

7

18

0.429

0.654

0.685

0.653

0.046**

mPdCIR016

5

8

0.602

0.479

0.545

0.548

−0.005

mPdCIR025

7

16

0.531

0.618

0.619

0.569

0.081

mPdCIR032

8

24

0.336

0.746

0.726

0.745

−0.026

mPdCIR035

5

14

0.628

0.526

0.547

0.431

0.212**

mPdCIR057

6

12

0.442

0.570

0.569

0.596

−0.049

mPdCIR063

6

16

0.372

0.689

0.698

0.734

−0.052

mPdCIR078

10

32

0.416

0.743

0.741

0.734

0.010

mPdCIR085

9

28

0.296

0.785

0.770

0.778

−0.010

PdAG1-ssr

15

49

0.283

0.842

0.822

0.793

0.036

PdAP3-ssr-F4

8

19

0.407

0.688

0.702

0.615

0.124*

PdCUC3-ssr1

1

1

1.000

0

0.000

0.000

N/A

PdCUC3-ssr2

13

31

0.358

0.785

0.784

0.633

0.193***

Average

6.9

17.5

0.541

0.548

0.557

0.531

0.038

Na number of alleles per locus, Ng number of genotypes per locus, Maf major allele frequency, Pic polymorphic information content, He expected heterozygosity, Ho observed heterozygosity, Fis inbreeding coefficient and Fis Wright’s analysis of hierarchical F-statistics, N/A not applicable

*p < 0.05, **p < 0.01, ***p < 0.001

aSupplementary Material Table S1

Amplification reactions were performed in a final volume of 20 μL containing 20 ng of DNA template, 4 pmol of reverse primer and 1 pmol of forward primer, 0.2 mM of each deoxynucleotide, 2 mM of MgCl2, and 1 unit of Taq polymerase (Sigma, USA). The forward primers were 5′-labeled with one of three fluorescent compounds (6-FAM, NED, or HEX) to enable analysis on automated sequencers. PCR was carried out using an Eppendorf Mastercycler pro vapo protect thermocycler (AG, Hamburg, Germany). After 5 min at 94 °C, 30 cycles were performed with 30 s at 94 °C, 60 s at the annealing temperature (depending on the locus), and 30 s at 72 °C, followed by a final extension step of 5 min at 72 °C. Amplified products were detected on an ABI 3130XL genetic analyzer (Applied Biosystems, USA). Analysis and allele calling were performed using the GeneMapper V3.7 software (Applied Biosystems, USA).

Data analyses

Genetic diversity analyses

PowerMarker v.3.25 (Liu and Muse 2005) was used to estimate the major allele frequency (Maf), the total number of genotypes (Ga), the number of alleles (Na), the number of alleles with a frequency higher than 5% (NAP), and the polymorphic information content (Pic) at each locus. The GenAlEx v.6.502 program (Peakall and Smouse 2012) was used to calculate the observed (Ho) and expected (He) heterozygosities as well as the inbreeding coefficient (Fis).

Date palm genetic relationships between populations

To investigate the genetic inter-population relationships, GeneAlex v.6.502 (Peakall and Smouse 2012) was used. The average number of alleles per locus (Na), the average number of alleles with a frequency higher than 5% (Nap), the allelic richness per locus (Ra), the observed heterozygosity, and the number of private alleles (Ar) within each population were estimated. Genetix v.4.0.5.2 (Belkhir et al. 2004) was used to estimate the inbreeding coefficient (Fis) and its significance within each population by using a bootstrap of 1,000,000 repetitions.

Genetic differentiation among and between the five Southeastern Nigerien subgroups by the 18 loci was estimated by calculating the Fst according to Weir and Cockerham’s estimate (Weir and Cockerham 1984) using GENEPOP v.4.2 (Rousset 2008). Fisher’s method was applied to test the significance of the pairwise Fst values (Raymond and Rousset 1995). The analysis of molecular variance (AMOVA) implemented in the GenAlEx v.6.502 program (Peakall and Smouse 2012) was conducted to estimate the hierarchical differentiation. GeneAlex v.6.502 (Peakall and Smouse 2012) was used to assign the various individuals of the Southeastern Nigerien population to the most likely population they could be native of.

To examine the relationships between the accessions of the five Southeastern Nigerien subgroups, the principal component analysis (PCA) with the factoMiner R package (Lê et al. 2008; Team R C 2016) was realized on the data of 18 markers. The genetic relationships among the genotypes of Southeast Niger, the Western genetic pool (Mauritania, Morocco, Tunisia, Libya, Sudan, and Egypt) and those of the Eastern genetic pool (Iraq, Pakistan, United Arab Emirates, and Oman), were examined by principal coordinate analysis (PCoA) carried out on the genetic distance matrix using the GenAlEx v.6.502 program (Peakall and Smouse 2012).

To deepen the knowledge on the origin of the Nigerien germplasm, the maternal and paternal lineages were studied. To this end, Western and Eastern chlorotypes (Henderson et al. 2006) and Y-haplogroup frequencies (Cherif et al. 2013) were calculated within the Nigerien sampling.

Genetic structure analysis

To identify the population structure of the date palm collection, we used a model-based clustering algorithm implemented in the computer program STRUCTURE v. 2.3.4 (Pritchard et al. 2000). This algorithm identifies clusters (K) with different allele frequencies and assigns portions of individual genotypes to these clusters. It assumes the Hardy-Weinberg equilibrium and linkage equilibrium within clusters. The STRUCTURE algorithm was run without previous information on the geographic origin of the accessions, using a model with admixture and correlated allele frequencies with 10 independent replicate runs for each K value (K value ranging from 1 to 6). For each run, we used a burn period of 10,000 iterations followed by 1,000,000 iterations. The optimal number of clusters was assigned by using the run with the maximum likelihood validated with an ad hoc quantity based on the second order rate of change in the log probability of data between different K values (Evanno et al. 2005). To obtain the optimal alignment of the independent iterations, CLUMPP v.1.1 (Jakobsson and Rosenberg 2007) implemented in the Pophelper software v.1.0.10 (Francis 2016) was used. Pophelper v.1.0.10 (Francis 2016) was also used to plot results for K = 2 to K = 6.

To generate hierarchical classifications, the shared allele distance (DAS) (Chakraborty and Jin 1993) between the Western and Eastern genetic pools and the Nigerien group was calculated. The obtained distance matrix was used to construct a phylogenetic tree using the neighbor-joining (NJ) algorithm. The bootstrap values were computed over 10,000 replications with the PowerMarker v.3.25 software (Liu and Muse 2005). The phylogenetic tree consensus got was thus confirmed via Mega software V7 (Kumar et al. 2016) and was then imported in Darwin software v.6 (Perrier and Jacquemoud-Collet 2006) in order to visualize the tree. Finally, the probability of belonging to one or another cluster at the level of three iterations (K = 3 which differentiates three groups of date palm) was formulated by the results of the STRUCTURE v. 2.3.4 software (Pritchard et al. 2000) allowing to create pie charts positioned on the phylogenetic tree.

Results

Polymorphism of microsatellite markers

A collection of 18 microsatellite primer pairs were used to analyze the genetic variation in the 113 Southeastern Nigerien date palm accessions. A total of 124 alleles were identified. The number of alleles per locus varied from 1 allele for PdCUC3-SSR1 to 15 alleles for PdAG1-ssr with an average of 6.9 alleles per locus (Table 1). Moreover, the number of genotypes per locus ranged from 1 for PdCUC3 SSR1 to 49 for PdAG1-ssr with an average of 18 genotypes per locus (Table 1). The major allele frequency per locus varied from 0.28 for PdAG1-ssr to 1 for PdCUC3-SSR1 with an average of 0.54 per locus. In addition, the polymorphic information content (PIC) at each locus ranged from 0 for PdCUC3-SSR1 to 0.84 for PdAG1-ssr with an average of 0.55 per locus (Table 1). The expected heterozygosity varied from 0 for PdCUC3-SSR1 to 0.82 for PdAG1-ssr with an average of 0.56 per locus while the observed heterozygosity varied from 0 for PdCUC3-SSR1 to 0.79 for PdAG1-ssr with an average of 0.53 per locus. The inbreeding coefficient (Fis) varied from −0.049 to 0.212 for mPdCIR057 and PdCUC3-SSR2, respectively, with an average of 0.04 per locus. Significant Fis values (p < 0.05, Table 1) were only obtained with the mPdIRD033, mPdCIR010, mPdCIR015, mPdCIR035, PdAP3-ssr-F4, and PdCUC3-SSR2 loci.

Genetic structure of Southeastern Nigerien date palms

Genetic relationships among the five Southeastern Nigerien date palm subgroups D. Takaya, Goure, Goudoumaria, Magariah, and Mirriah

Here, the results are reported for each of the subgroups. The average number of alleles per locus ranged from 4.17 for the D. Takaya subgroup to 6 for Goure with an average of five alleles per locus for each subgroup (Table 2). For all subgroups, the average number of alleles with a frequency higher than 5% was 3.71 alleles per locus (Table 2). The allelic richness was almost identical for the five subgroups with an average of 2.96 alleles per locus (Table 2). The expected heterozygosity was almost identical for the five subgroups with an average of 0.56. It was the same for the observed heterozygosity with an average of 0.53. The Fis of all subgroups was significantly positive (p < 0.05). It varied from 0.026 to 0.119 for Goudoumaria and D. Takaya, respectively, with an average of 0.075 for all groups (Table 2).
Table 2

Date palm genetic diversity in five cultivation departments in Southeast Niger

Population

N

Na

Nap

Ar

Pa

He

Ho

Fis

D. Takaya

12

4.17

3.44

2.76

4.17

0.56

0.51

0.119*

Goudoumaria

13

4.33

3.33

2.84

4.33

0.54

0.55

0.026*

Goure

32

6.00

3.50

3.08

6.00

0.56

0.53

0.075*

Magariah

39

5.94

4.28

3.18

5.94

0.58

0.54

0.073*

Mirriah

17

4.83

4.00

2.96

4.83

0.55

0.52

0.083*

Average

22.6

5.06

3.71

2.96

5.06

0.56

0.53

0.075*

D. Takaya Damagaram Takaya, N number of accessions, Na number of alleles per locus, Nap number of alleles with a frequency higher than 5%, Ar allelic richness, Pa private alleles, He expected heterozygosity, Ho observed heterozygosity, Fis fixation index values

*p < 0.05

In general, the values of shared allele distance and genetic differentiation coefficient (Fst) among the subgroups from the five departments were very low. However, the lowest shared allele distance and Fst were observed between Magariah and Goure that appeared to be close to each other, whereas the highest values were observed between D. Takaya and Goudoumaria which seemed more genetically distant (p < 0.05, Table 3).
Table 3

Shared allele distance (above the diagonal) and Fst (below the diagonal) of five date palm groups from Southeast Niger

Group

D. Takaya

Goudoumaria

Goure

Magariah

Mirriah

D. Takaya

0.000

0.301

0.238

0.231

0.286

Goudoumaria

0.050*

0.000

0.225

0.225

0.216

Goure

0.029*

0.028*

0.000

0.148

0.178

Magaria

0.030*

0.026*

0.009*

0.000

0.157

Mirriah

0.047*

0.028*

0.015*

0.011

0.000

D. Takaya Damagaram Takaya

*p < 0.05

Based on the analysis of molecular variance (AMOVA), the observed genetic diversity was explained through individual variations (100%), and no intergroup variation was observed (p < 10−4, Table 4).
Table 4

AMOVA for date palm differentiation based on 18 microsatellite markers

Source

df

Sum of square

Estimated variability

% of variation

Among grp

4

1.923

0.000

0*

Among indiv

108

50.152

0.000

0*

Within indiv

113

53.500

0.473

100*

Total

225

105.575

0.474

100*

df degree of freedom

*p < 0.001

Genetic relationships between the individuals of the five Nigerien subgroups

Considering the two first components of the principal component analysis (PCA), none of the 113 date palm accessions of the five subgroups was distinguished a posteriori. The gravity centers of these groups were not only close to each other, but were also close to the origin of the two components (Fig. 2).
Fig. 2

Principal component analysis (PCA) of 113 date palm accessions from the five subgroups. The two first components explain 40.3% of the total variation

Genetic relationship between Nigerien date palms and the Western and Eastern pools

The principal coordinate analysis (PCoA) of the 361 date palm accessions from the Nigerien pool, the Western pool (Mauritania, Morocco, Tunisia, Libya, Sudan, and Egypt), and the Eastern pool (Iraq, Pakistan, United Arabic Emirates, and Oman) showed that component 1 opposed the populations of the Eastern pool to both the Western and the Nigerien ones (Fig. 3). Component 2 differentiated the accessions of the same gene pools, Western germplasm being more diverse than the Eastern (Fig. 3).
Fig. 3

Principal coordinate analysis (PCoA) of the date palm accessions from the Eastern genetic pool (Iraq, Pakistan, United Arab Emirates, and Oman) in red, the Western genetic pool (Mauritania, Morocco, Tunisia, Libya, Sudan, and Egypt) in green, and the Southeastern Nigerien populations in blue

The assignments of the Southeastern Nigerien genotypes showed that 91% of these genotypes were actually assigned to the Nigerien group and the remaining 9% were assigned to the Western genetic pool (Table 5).
Table 5

Nigerien date palm assignments

Origin

Assignment

Population (%)

Niger

103

91

Eastern pool

0

0

Western pool

10

9

Maternal and paternal lineages of the five subgroups from Southeast Niger

The chloroplast minisatellite showed two chlorotypes, i.e., the 242 and the 254, corresponding to the Western and Eastern maternal lineages, respectively (Pintaud et al. 2010). In the Nigerien date palm group, both chlorotypes were detected. The Western chlorotype 242, however, was the most common with frequencies varying from 0.76 for the Mirriah subgroup to 1 for the Goudoumaria subgroup. The highest frequency of the Eastern chlorotype 254 was observed in the Mirriah subgroup with 0.23 (Fig. 4a).
Fig. 4

Maternal and paternal lineage distribution within Southeastern Nigerien date palm groups. a Chlorotype distribution, the green and red histograms correspond to the Western (242) and Eastern (254) chlorotypes, respectively. b Y haplotype distribution, the green and red histograms correspond to Western and Eastern haplotypes, respectively

The Y haplogroups were formed by two Western haplotypes and one Eastern haplotype. The frequency of the first Western Y haplotype (180-191-192) varied from 0.17 in the D. Takaya subgroup to 0.50 in the Mirriah and Magariah subgroups (Fig. 5). The second Western Y haplotype (180-193-192) frequencies varied from 0.38 for the Magariah subgroup to 0.83 for the D. Takaya subgroup. The Eastern Y haplotype (180-188-308) was only observed in the Magariah subgroup with a frequency of 0.13 (Fig. 4b). The sampling of Goure and Goudoumaria subgroups was entirely composed by female genotypes, meaning that here no Y haplotype was identified at all (Fig. 4b).
Fig. 5

Inferred population structure for K = 2 to K = 6 as the presumed number of subpopulations within the date palm collection, including 361 accessions. Each individual is represented by a vertical bar, partitioned into colored segments representing the proportion of the individual’s genome in the K clusters. The date palm groups are separated by white dotted lines

Model-based Bayesian clustering analysis of date palm Southeast Niger and Old World genetic information

The model-based Bayesian clustering approach implemented in STRUCTURE v. 2.3.4 (Pritchard et al. 2000) was used to investigate the genetic structure of date palm genotypes according to the models with two (K = 2) to six clusters (K = 6). The change of rate in the log likelihood between successive K values (∆K = 225) revealed a first level of clustering at K = 3 for the studied date palm accessions (Fig. 5; Supplementary Material Table S2, Fig. S1).

At K = 2, the date palm accessions were differentiated into two geographic clusters, the first cluster consisting of accessions from the Eastern pool and the second cluster consisting of accessions from the Western pool as well as the Southeastern Nigerien group (Fig. 5). At K = 3, the accessions from Southeast Niger were separated from those of the Western pool. At K = 4, the Egyptian, Libyan, Mauritanian, and Moroccan groups were separated from the other Western accessions.

At K = 5 and K = 6, the genetic structure of the date palm accessions was mainly the same and no meaningful additional cluster was observed (Fig. 5).

The shared allele distance and Fst calculated from the 18 markers showed the lowest values between the Southeastern Nigerien and the Tunisian populations (p < 10−4, Table 6). However, the highest values of these distances were recorded among the populations of Southeast Niger and the UAE (p < 10−4, Table 6).
Table 6

Shared allele distance (Das) and Fst between the Southeastern Nigerien populations and the 11 populations of the two Eastern and Western genetic pools

Country

Distance

Eg

Ir

Li

Ma

Mc

Om

Pak

So

Tu

UAE

Niger

Das

0.290

0.418

0.374

0.291

0.252

0.465

0.421

0.411

0.198

0.459

Fst

0.053*

0.115*

0.096*

0.020*

0.036*

0.146*

0.119*

0.105*

0.032*

0.150*

Eg Egypt, Ir Iraq, Li Libya, Ma Mauritania, Om Oman, Pak Pakistan, So Sudan, Tu Tunisia, UAE United Arab Emirates

*p < 10−4

Genetic relationships among the predefined date palm groups were also assessed based on the DAS genetic distances and the NJ algorithm (Fig. 6). Each pie chart represented with a country on the phylogenetic tree represents the probability of its population to belong to one from the three groups found with the STRUCTURE software at K = 3, with red indicating the group of the UAE and Oman populations, yellow the Nigerien population, and green the Tunisian population (Fig. 6). According to the bootstrap values, the 11 date palm groups were classified into two clusters: cluster I, including Niger, Mauritania, Morocco, Sudan, Libya, Tunisia, and Egypt and thus corresponding to the Western cluster, was clearly distinguished from cluster II (or the Eastern cluster), including Oman, Iraq, the UAE, and Pakistan, by a high bootstrap support of 100% (Fig. 6). Moreover, the Southeastern Nigerien population was closer to the Tunisian one (86%) (Fig.6). However, the low bootstrap values between the other populations revealed that the topography of the phylogenetic tree is not well supported in the Western cluster and needs further studies including increased sampling.
Fig. 6

NJ clustering of geographic groups based on the DAS genetic distance values, as well as the distribution of the genetic clusters within each of them. The colors correspond to the genetic clusters defined by the STRUCTURE analysis, as reported in Fig. 5. The numbers next to the nodes indicate the bootstrap support percentages in 10,000 pseudoreplicates

Discussion

Knowledge of genetic resources of cultivated species is of great importance to improve productivity and efficiency of any activity tending to its preservation and valorization. Information on date palm genetic diversity in the Sahel, considered as a marginal area for date production, is at the heart of this study. With the current trend of climate change in the Sahel (de Sherbinin 2014) and the decline of isohyet 300 mm to more than 200 km further to the South (Ozer et al. 2010), date palm cultivation will be particularly suitable in this area in the future.

The genetic diversity of 113 Nigerien date palm accessions revealed a total of 124 alleles with a mean of 6.9 alleles per locus. The average of expected heterozygosity (0.56) is comparable to that found in Tunisia by Zehdi-Azouzi et al. (2016), but remains lower than those found in Libya (Racchi et al. 2014) and in Sudan (Elshibli and Korpelainen 2008). These results show a high genetic diversity in the date palm germplasm of Southeast Niger.

Our results clearly indicate that the five Southeastern Nigerien subgroups have a homogeneous genetic diversity and consequently behave as a single metapopulation. The analysis of molecular variance shows that the variations noticed inside this single group result from individual molecular differences only. The result of homogeneous genetic diversity is supported by several results such as the number of alleles per locus per subgroup, the shared distances, and the index of genetic differentiation (Fst) between these subgroups. In addition, the analysis of principal component also confirms this result. Compared with the palm groves of Tunisia (Zehdi et al. 2012; Zehdi-Azouzi et al. 2016) in which 5% of the genetic variation is due to geographical grouping, the palm groves of Southeast Niger show a more homogeneous genetic diversity with 0% of variation due to its geographic origin. Our results, in line with those of Lenormand (1984), confirm the same genetic background behind the Damagaram and Manga date palm populations.

The Nigerien germplasm is an integral part of the Western genetic pool as revealed by nuclear markers. Moreover, the analysis of the female lineage confirms the maternal Western origin of the Nigerien palms where 92% of the chlorotypes are occidental (chlorotype 242, Pintaud et al. 2013; Zehdi-Azouzi et al. 2015, 2016) and only 8% of the chlorotypes show an oriental origin (chlorotype 254, Pintaud et al. 2013; Zehdi-Azouzi et al. 2015, 2016). The analysis of the paternal lineage shows the same pattern with a large proportion of the Western haplogroup A (92%) (Cherif et al. 2013) and a low percentage of the Eastern haplogroup B (8%) (Cherif et al. 2013). These results provide additional evidence of the belonging of the Southeastern Nigerien germplasm to the Western genetic diversity with a low Eastern introgression. Taken together, our results show the extension of the Western gene pool previously defined in North Africa (Zehdi-Azouzi et al. 2015) to the South in the Sahelian region. However, the main question of the western genetic pool’s origin remains unsolved.

Date palm introduction in the Southeast Niger may date from the years 1917 to 1918 during the French colonial era from seeds from Aïr, Djado, or Fezzan in Libya (Munier 1963; Lenormand 1984; Jahiel 1996). However, it is also possible that it has existed prior to early twentieth century given the fact that the main route linking North Africa to Northern Nigeria passes through the Saharan palm groves of Bilma and the current study area of Manga (Zakari 1985). Even though the mission of Foureau (1902) reported no date palm on its route in the Southeast Niger, it would be reasonable to think that there would have been some date palms in oasis basins which had been established in strategic points to water and feed the caravan camels (Zakari 1985). The Southeastern Nigerien date palms could be an ancient local population or come from another origin within the Western genetic pool, which remains to elucidate.

Conclusion

This study also highlights the originality of the Southeastern Nigerien date palm population, which constitutes a new Sahelian group. Furthermore, it establishes a secondary genetic structure within the Western gene pool. To better understand the Sahelian group’s origin and define its extent, it is necessary to undertake a complete genetic analysis of date palm groves in the region from the Northeast of the country, the nearby South of Algeria, and from other countries of the Sahelian area.

Notes

Acknowledgments

This article is dedicated to our colleague and friend Dr. Jean-Christophe Pintaud who passed away prematurely. This work was granted by the IFS (International Foundation of Science, D / 5695-1, 2014), CIRAD (France, AI N°1 2014; 2015 and 2016) for the field work, the French Embassy in Niger, and the Government of Niger. This study was made possible by grant NPRP-EP X-014-4-001 from the Qatar National Research Fund (a member of the Qatar Foundation), ANR Phoenix, and ISEM. We thank Mr. Garkoua Sayédi, the hydraulic Magariah director; Col Barmou Hamza, the director of Goure environment; Mr. Elh Idi, the village chief of Killakina; and Mr. Mamane Moussa, the regional coordinator of NGO Karkara Zinder for their logistical support. We also thank M. Hassan Shabana, Ali Zouba, Karim Kadri, Ahmed Othmani, Claire Newton, Jean-Frederic Terral, and Sarah Ivorra for providing the plant material.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

The list of accession numbers is in the Supplementary Material (Table S3).

Supplementary material

11295_2017_1150_MOESM1_ESM.docx (112 kb)
ESM 1 (DOCX 111 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Oumarou Zango
    • 1
    • 2
    • 3
  • Emira Cherif
    • 1
  • Nathalie Chabrillange
    • 1
  • Salwa Zehdi-Azouzi
    • 4
  • Muriel Gros-Balthazard
    • 5
  • Summar Abbas Naqvi
    • 6
  • Alain Lemansour
    • 7
  • Hervé Rey
    • 2
  • Yacoubou Bakasso
    • 3
  • Frédérique Aberlenc
    • 1
  1. 1.IRD, UMR DIADE-F2F, Centre IRDMontpellierFrance
  2. 2.CIRAD, UMR AMAPMontpellierFrance
  3. 3.Faculty of Sciences and TechnologiesAbdou Moumouni UniversityNiameyNiger
  4. 4.Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et BiotechnologieUniversité de Tunis El ManarEl ManarTunisia
  5. 5.Institut des Sciences de l’Evolution de Montpellier, UMR 5554, Equipe Dynamique de la biodiversité, anthropo-écologieMontpellier cedex 05France
  6. 6.University of AgricultureInstitute of Horticultural SciencesFaisalabadPakistan
  7. 7.Date Palm Development Research Unit, Plant Tissue Culture LaboratoryAl AinUAE

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