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Heterochromatin distribution and comparative karyo-morphological studies in Vigna umbellata Thunberg, 1969 and V. aconitifolia Jacquin, 1969 (Fabaceae) accessions
expand article infoAnju Shamurailatpam, Latha Madhavan§, Shrirang Ramachandra Yadav|, Kangila Venkatraman Bhat, Satyawada Rama Rao
‡ North Eastern Hill University, Shillong, India
§ NBPGR, Regional Station, Thrissur, India
| Botany Department, Shivaji University, Kolhapur, India
¶ NRC on DNA Fingerprinting, NBPGR, Pusa Campus, Delhi, India
Open Access

Abstract

Chromosome studies along with heterochromatin distribution pattern analysis have been carried out in two domesticated species of Vigna Savi, 1824 which grow in contrasting geo-climatic conditions of India: Vigna umbellata Thunberg, 1969, a legume well acclimatized to subtropical hilly regions of North-east India and V. aconitifolia Jacquin, 1969, a species of arid and semi-arid regions in desert plains of Western India. Karyo-morphological studies in both species reveal 2n = 22 chromosomes without any evidence of numerical variation and the overall karyotype symmetry in chromosome morphology suggest that the diversification at intraspecific level in genus Vigna has occurred through structural alteration of chromosomes, rather than numerical changes. Heterochromatin distribution as revealed by fluorochrome binding pattern using CMA3 and DAPI, confirms the occurrence of relatively more GC content in V. aconitifolia as compared to V. umbellata. However, AT content was found to be comparatively higher in V. umbellata which perhaps play a role in species interrelationships.

Keywords

Asymmetry index, C-heterochromatin, Fabaceae, karyotype, NOR-chromosomes, Vigna

Introduction

The pantropical genus Vigna Savi, 1824 (Fabaceae) includes 104 described species (Lewis et al. 2005). Among its subgenera, only Ceratotropis Marechal, 1978 is known for its rich species diversity in Asia (Verdcourt 1970, Marechal et al. 1978, Tateishi 1996). Tomooka et al. (2002) recognized 21 species in the subgenus Ceratotropis, out of which six species are domesticated: azuki bean (V. angularis Willdenow, 1969), mung bean (V. radiata Linnaeus, 1954), black gram (V. mungo Linnaeus, 1956), rice bean (V. umbellata Thunberg, 1969), moth bean (V. aconitifolia Jacquin, 1969) and creole bean (V. reflexo-pilosa var. glabra Marechal, 1911). The genetic resources and diversity in cultivated and wild forms of subgenus Ceratotropis occurring in Indian subcontinent are extremely rich and interesting (Bisht et al. 2005). The domesticated V. aconitifolia is confined only to the tropical region of India, while V. umbellata is widely domesticated across the South-east Asia. The origin of V. umbellata is considered to be Indo-China region and also to a certain extent from South-east Asia (Marechal et al. 1978, Baudoin and Marechal 1988).

The structure and morphology of the chromosomes are of vital importance when studying the origin, evolution and classification of taxa (Yang et al. 2005) as well as distance or relatedness among diverse genomes (Stace 2000, Kumar and Rao 2002). Quite a few number of reports dealing with such studies are available for Vigna species (Rao and Chandel 1991, Rao and Raina 2004, Shamurailatpam et al. 2012).

Chromosome location and characterization of C-heterochromatin by fluorescence staining procedures which preferentially stain GC-rich DNA and DAPI, which localised AT-rich regions has been successfully applied in a large number of Fabaceae taxa including Cicer arietinum Linnaeus, 1753 (Galasso et al. 1996a); Phaseolus calcaratus Roxburgh, 1832 (Zheng et al. 1991); Sesbania tetraptera Hochstetter, 1871 (Forni-Martins et al. 1994, Forni-Martins and Guerra 1999); Vicia faba Linnaeus, 1753 (Greilhuber 1975); Vigna ambacensis Welwitsch, 1978 (Galasso et al. 1996b).

A certain degree of chromosomal variation at inter-specific level of the genus Vigna has been documented using cytogenetic approaches by earlier workers (Rao and Chandel 1991, Shamurailatpam et al. 2012). Hence, it will be quite significant to see the extent of variation among the domesticated species of Vigna (Ceratotropis). V. umbellata is a species domesticated extensively in the subtropical hilly and moist regions of North-east India. On the other hand, V. aconitifolia has been adapted to the arid and semi-arid region of tropical Western plain of India. Analysis of karyo-morphological details in V. umbellata and V. aconitifolia, adapted to extremely contrasting environmental conditions, may ultimately help us to define their chromosome variation. Meaningful propagation programs can be developed from such information.

Materials and methods

Karyo-morphological studies were undertaken in ten accessions each of V. umbellata and V. aconitifolia. The germplasm has been obtained from Indian Council of Agricultural Research (ICAR), Baranapi, Meghalaya and also from National Bureau of Plant Genetic Resources (NBPGR), New Delhi. Actively growing root tips of about 1–2 cm long were excised from germinating seeds on moist filter paper in Petri dishes at 25 ± 2 °C, pre-treated with 0.025% colchicine (Himedia) for 3 h at room temperature (20 ± 2 °C). The root tips after pre-treatment were fixed in freshly prepared ethanol-acetic acid (v/v, 3:1) and subsequently stored at 4 °C until required. For slide preparation, the root tips were washed twice in distilled water, hydrolyzed in 1N HCl at 60 °C for 8 min and stained in Feulgen stain (leuco-basic fuchsin) for 45 min. The stained root tips were thoroughly washed and subsequently squashed in 1% acetocarmine. The micro-photographs of the metaphase plates were taken from both temporary and permanent preparations. At least 10–15 clear preparations of chromosome complements of each species were analyzed. Photo-idiograms were prepared from photomicrographs by cutting out individual chromosome and arranging them in descending order of their length and matching on the basis of morphology, the chromosomes were resolved into 11pairs. The standard method of chromosome classification given by Battaglia (1955) classification of metacentric / median (V), submetacentric/ submedian (L), subtelocentric (J) and telocentric (I) based on the arm ratio of 1:1, >1:1<1.3, >1:3<1:0 and 1:0 respectively was employed for comparison. The degree of asymmetry was estimated by means of the parameters proposed by Peruzzi and Eroğlu (2013): Coefficient of Variation of Chromosome Length (CVCL) and Mean Centromeric Asymmetry (MCA).

For heterochromatin characterization, root-tips were digested in 2% cellulase and 20% pectinase solution for 180 min at 37°C. Meristems were washed in distilled water, squashed in a drop of 45% acetic acid, and frozen in liquid nitrogen. The slides were stained with DAPI (2 µg/ml): glycerol (1:1, v/v) solution to allow selection of the best plates. Subsequently, they were destained in ethanol: glacial acetic acid (3:1, v/v) for 30 min and transferred to absolute ethanol for 1 h, both at room temperature. Slides were air-dried and aged for 3 days at room temperature. The slides were stained with CMA3 (0.5 mg/ml, 1 h) and DAPI (2 µg/ml, 30 min), mounted in McIlvaine’s buffer (pH 7.0): glycerol (1:1, v/v), and stored for 3 days (Schweizer and Ambros 1994). Slides were analyzed under Leica DM 4000 B microscope and photographs were carried out with different filter combinations using Leica CCD camera.

Results

The somatic chromosome number of all the accessions had consistently 2n = 2x = 22 (Fig. 1). The chromosome complements were resolved into 11 pairs which formed a graded series from longest to shortest within the idiograms. A noticeable difference in length between the longest and the shortest chromosomes within the complement was recorded (Table 1). The longest chromosome of the haploid complement was almost 2.5 times longer than the shortest one in V. aconitifolia accessions, while it was 2 times longer than the shortest one in V. umbellata accessions. Further investigated accessions belonging to V. umbellata and V. aconitifolia had metacentric, submetacentric and subtelocentric chromosomes in their respective chromosome complements. Submetacentric chromosomes outnumbered the metacentric ones in V. aconitifolia accessions while metacentric chromosomes outnumbered the submetacentric chromosomes in the case of V. umbellata accessions.

Various accessions of these species have shown distinctive variation in the karyotype with respect to number of metacentric and submetacentric chromosomes (Fig. 2). Subtelocentric chromosomes were found in V. aconitifolia but not in V. umbellata accessions. Heteromorphic chromosome and nucleolar chromosomes are recorded in the accessions of both V. umbellata and V. aconitifolia.

Figure 1.

Mitotic complements of 10 accessions of V. umbellata. a–j: a BKSB 205 b TRB 160 c RBS 35 d IC 551699 e BKSB 192 f RBS 53 g IC 55440 h IC 176563 i EC 97882 j BKSB 194 k–t: k IC 36157 l VDV 6175 m IC 472147 n RM 040 o IC 39809 p IC 285159 q IC 36592 r IC 472173 s IC 39713 t IC 36562. Bar = 5 μm.

Figure 2.

Photo-idiograms of a–j 10 accessions of V. umbellata a BKSB 205 b TRB 160 c RBS 35 d IC 551699 e BKSB 192, f RBS 53 g IC 55440 h IC 176563 i EC 97882 j BKSB 194 k–t 10 accessions of V. aconitifolia k IC 36157 l VDV 6175 m IC 472147 n RM 040 o IC 39809 p IC 285159 q IC 36592 r IC 472173 s IC 39713 t IC 36562. Heteromorphic groups marked above the short arm and nucleolar groups are marked below the long arm.

Karyomorphology and arm ratio in studied taxa of Vigna.

Sl. no. Species Accessions no. 2n Chromosome arm length (L/S ratio) Ratio of longest and shortest chromosome Karyotype formula
I II III IV V VI VII VIII IX X XI
1 V. umbellata BKSB 205 22 1.12
1.14
1.8 1.5 1.5 1.25 1 1.3 1.3 1.3 1.3 1.3 2.4 2V + 20L
2 V. umbellata TRB 160 22 1.2
1.5
1.1
1.25
1.75 1.37 1 1 1 1.3 1.3 1 1 2.2 12V + 10L
3 V. umbellata RBS 35 22 1.2 1.6 1 1 1 1 1 1.15 1.3 1.3 1 2.8 12V + 10L
4 V. umbellata IC 551699 22 1
1
1.3 1.7 1.15 1.57 1.75 1.1 1 1 1 1 4.0 12V + 10L
5 V. umbellata BKSB 192 22 1 1 1 1.25 1.12 1 1 1 1.3 1 1 2.0 16V + 6L
6 V. umbellata RBS 53 22 1.2 1.1 1.25 1.25 1 1 1 1 1.3 1.3 1 2.3 12V + 10L
7 V. umbellata IC 55440 22 1.57
1.42
1.2 1.35 1.12 1.12 1.12 1 1 1 1.15 1.3 3.0 6V + 16L
8 V. umbellata IC 176563 22 1.14
1.28
1.6 1.1 1.25 1.6 1.3 1 1 1.6 1.3 1 2.6 8V + 14L
9 V. umbellata EC 97882 22 1.7 1.47 1.2 1.37 1.2 1 1 1.65 1.3 1.3 1 2.3 8V + 14L
10 V. umbellata BKSB 194 22 1 1 1 1.3 1.3 1.3 1.3 1.3 1 1 1 3.0 12V + 10L
11 V. aconitifolia IC 36157 22 1.33 1.9 2 1.5 1.1
1.5
1.5 1.5 1.5 1 1 1 1.75 6V + 16L
12 V. aconitifolia VDV 6175 22 1.5
1.66
2.5 1.33 2 1.5 1.5 1.5 1.5 1.25 1 1 2.5 4V + 16L + 2J
13 V. aconitifolia IC 472147 22 2 2.5 2.5
2
1 1 1 1.5 1.75 1.5 1 1 2.25 10V + 12L
14 V. aconitifolia RM 040 22 1.5 1.66 3
2
1.5 2 2 1.75 1.25 1.5 1.5 1 2.5 2V + 18L + 2J
15 V. aconitifolia IC 39809 22 1.57 2 1.66 1.33 2 1.16 1 1.25 1.25 1.5 1 3.0 4V + 18L
16 V. aconitifolia IC 285159 22 1.33 2 1.5 1.5 1 1.5 1.25 1 1 1 1 3.5 10V + 12L
17 V. aconitifolia IC 36592 22 1.75
1.6
1.62 1 1 1.66 1 1 1.33 1.33 1 2 2.16 10V + 12L
18 V. aconitifolia IC 472173 22 2.4
1.8
1.83
2
1.86 1.25 1.12 1 1 1 1 1 1 4.25 14V + 8L
19 V. aconitifolia IC 39713 22 2 2.5 1 2 1 1.5 1.5 1.5 1.5 1.5 1 2.25 6V + 16L
20 V. aconitifolia IC 36562 22 1.58 3 1.49 1.33 1 1 1 1.5 1.5 1.5 1 2.5 8V + 14L

Karyotype formulae and characteristics in the studied taxa of Vigna. SC the shortest chromosome length; LC the longest chromosome length; CL mean length of chromosome; CI mean centromeric index; SD standard deviation; CVCL component expressing the relative variation in chromosome length; MCA mean centromeric asymmetry.

Sl. no. Accessions no. 2n Range
SC-LC (μm)
Ratio
LC/SC
CL (μm)
Mean (± SD)
CI Mean (± SD) CVCL MCA
1 BKSB 205 22 17-7 2.4 9.13 (± 2.76) 42.87 (± 3.47) 30.25 14.30
2 TRB 160 22 11-5 2.2 7.95(± 1.55) 45.22 (± 4.65) 19.59 9.09
3 RBS 35 22 17-6 2.8 9.18(± 2.95) 46.93 (± 3.85) 32.19 6.18
4 IC 551699 22 24-6 4 11.5(± 4.3) 45.59 (± 5.03) 37.4 9.06
5 BKSB 192 22 12-6 2 8.45(± 1.78) 48.57 (± 2.49) 21.16 2.81
6 RBS 53 22 14-6 2.3 8.40(± 1.74) 47.09 (± 2.91) 20.72 5.78
7 IC 55440 22 18-6 3 9.31(± 2.99) 46.55 (± 2.92) 32.13 6.49
8 IC 176563 22 16-6 2.6 9.18(± 2.66) 44.29 (± 4.65) 29.02 11.37
9 EC 97882 22 14-6 2.3 9.18(± 2.27) 44.94 (± 3.94) 24.82 55.07
10 BKSB 194 22 18-4 3 7.09(± 1.62) 46.75 (± 3.55) 22.86 6.49
11 IC 36157 22 7-4 1.75 5.22 (± 1.04) 42.44 (± 6.07) 19.92 15.32
12 VDV 6175 22 10-4 2.5 5.68 (± 1.54) 40.76 (± 7.06) 27.25 18.55
13 IC 472147 22 9-4 2.25 5.81 (± 1.36) 41.61 (± 8.54) 23.54 16.51
14 RM 040 22 10-4 2.5 6.09 (± 1.67) 38.78 (± 6.45) 27.52 22.88
15 IC 39809 22 12-4 3 6.72 (± 2.02) 42.04 (± 6.17) 30.12 16.22
16 IC 285159 22 7-2 3.5 4.68 (± 1.25) 43.63 (± 5.72) 26.85 10.8
17 IC 36592 22 11-6 2.16 7.95 (± 1.60) 43.89 (± 6.32) 20.22 12.21
18 IC 472173 22 17-4 4.25 8.59 (± 3.66) 44.99 (± 7.29) 42.64 10.14
19 IC 39713 22 9-4 2.25 5.72 (± 1.28) 40.47 (± 6.85) 22.44 19.05
20 IC 36562 22 10-4 2.5 6.22 (± 1.47) 43.34 (± 8.09) 23.68 15.13

Telocentric chromosomes were absent in both the taxa studied. Heteromorphic chromosomes were observed in some of the V. umbellata accessions: BKSB 205 (1st pair, Fig. 2a), TRB 160 (1st and 2nd pair, Fig. 2b), IC 551699 (1st pair, Fig. 2d), IC55440 (1st pair, Fig. 2g) and IC 176563 (1st pair, Fig. 2h). In V. aconitifolia heteromorphic chromosomes were found in IC 36157 (5th pair, Fig. 2k), VDV 6175 (1st pair, Fig. 2l), IC 472147 (3rd pair, Fig. 2m), RM040 (3rd pair, Fig. 2n), IC 36592 (1st pair, Fig. 2q) and IC 472173 (1st and 2nd pair, Fig. 2r) accessions. Nucleolar Organizing Regions (NORs), as a secondary constriction/satellites, were observed in V. umbellata accessions RBS 35 (1st pair, Fig. 2c), IC 551699 (2nd pair, Fig. 2d), and EC 97882 (3rd and 4th pair, Fig. 2i). Vigna umbellata was characterized by the presence of both metacentric and submetacentric chromosomes and two V. aconitifolia accessions (VDV 6175 and RM 040) were characterized by the presence of distinct subtelocentric chromosome, though their position differed in karyotype. The remaining accessions were devoid of any subtelocentric chromosome.

According to the scatter plot obtained by CVCL vs. MCA, BKSB 192 (V. umbellata) and EC 97882 (V. umbellata) showed the lowest (2.81) and highest (55.07) MCA respectively (Fig. 4). Furthermore IC 285159 (V. aconitifolia) and RM 040 (V. aconitifolia) showed lowest (10.8) and highest (22.88) MCA values. In V. umbellata TRB 160 and IC 551699 exhibited lowest (19.59) and highest (37.4) CVCL values. Among V. aconitifolia accessions IC 36157 and IC 472173 had shown lowest (19.92) and highest (42.64) CVCL values.

A comparative account of heterochromatin distribution pattern within the chromosome complements in V. umbellata and V. aconitifolia has been summarized in Table 3 and the data have been illustrated in Fig. 3. The CMA3+ and DAPI+ binding sites were found either in terminal or in interstitial regions, in both the taxa studied. V. umbellata had more of DAPI+ sites 3.1(± 1.9) in the interstitial region of the chromosomes and the terminal binding sites were 1.8(± 0.6). The number of chromosomes showing different CMA+ and DAPI+ sites also ranged from 2–7 in this species. On the other hand, in V. aconitifolia the heterochromatin block comprised more of CMA+ binding sites 2.9(± 1.3), which were found in the terminal region of the chromosomes while 2(± 1.2) binding sites were interstitial in position. The number of chromosomes showing CMA+ sites ranged from 3–7, while those showing the DAPI+ sites ranged from 3–8.

Figure 3.

Differentially stained mitotic chromosomes complements a–b V. umbellata c–d V. aconitifolia. Arrows indicate CMA+ and DAPI+ sites. Scale bar = 5 µm in all the figures.

Figure 4.

Scatter plot based on the karyotype parameters MCA (x axis) vs. CVCL (y axis) a BKSB 192 b RBS 53 c RBS 35 d BKSB 194 e IC 55440 f IC 551699 g TRB 160 h IC 472173 i IC 285159 j IC 176563 k IC 36592 l BKSB 205 m IC 36562 n IC 36157 o IC 39809 p IC 472147 q VDV 6175 r IC 39713 s RM 040 t EC 97882.

Distribution of CMA+ and DAPI+ sites in the chromosomes of Vigna species.

Species Mean± SD of CMA+ sites in chromosomes Mean± SD of DAPI+ sites in chromosomes Range of CMA+ sites Terminal Range of DAPI+ sites Interstitial
Terminal Interstitial Terminal Interstitial
V. umbellata 1.7 ± 0.8 2.1 ± 0.8 1.8 ± 0.6 3.1 ± 1.9 1.7 ± 0.8 2.1 ± 0.8
V. aconitifolia 2.9 ± 1.3 2 ± 1.2 2.7 ± 0.7 2.3 ± 0.8 2.9 ± 1.3 2 ± 1.2

Discussion

The present data, combined with the chromosome counts available from the literature confirm the somatic chromosome number of 2n = 22 for both species, V. umbellata and V. aconitifolia. Such observation received support from reports of Singh and Roy (1970), Rao and Chandel (1991), Rao and Raina (2004), Shamurailatpam et al. (2012). The presence of subtelocentric chromosomes in V. aconitifolia accessions is in agreement with the earlier report of Sinha and Roy (1979).

All the accessions of V. umbellata and V. aconitifolia have shown no deviation in somatic chromosome numbers and overall karyotype appearance. However, V. umbellata had a higher degree of karyotype asymmetry as compared to V. aconitifolia, suggesting structural rearrangements in karyotypes. Hence, the observed karyotype variation is likely to have originated by structural changes in chromosomes vs. duplication, deletions, interchanges and inversions (Stebbins 1971, Rao and Chandel 1991). Thus, structural alteration of the chromosomes involving centric fusion and centromere repositioning might have influenced the speciation in genus Vigna.

Due to the very small size of chromosomes accompanied by technical difficulties, the nucleolus organisers among the chromosome complements could not be clearly resolved. Other cytogenetic techniques such as silver staining and fluorescence in situ hybridization (FISH) can be useful in detecting NOR-loci on chromosomes.

The DAPI+ binding sites in chromosomes, which are indicative of AT-rich region, were recorded in the interstitial regions of chromosomes in V. umbellata. However CMA+ sites, found mostly in V. aconitifolia chromosomes, suggest that the heterochromatin blocks were rich in GC base composition at terminal regions of chromosomes. The higher distribution of AT- and GC- repetitive sequence in heterochromatin blocks is probably reflecting the processes of divergent evolution of repetitive sequences, in heterochromatin regions of Vigna species (Shamurailatpam et al. 2014).

In the course of evolution, most of the heterochromatin regions tend to increase (Ikeda 1988), this phenomenon is also observed in Vigna (Shamurailatpam et al. 2015). Certain genera such as Vicia, Phaseolus, Sesbania, Cicer and Vigna (Greilhuber 1975, Zheng et al. 1991, Forni-Martins et al. 1994, Galasso et al. 1996a, b, Forni-Martins and Guerra 1999) showed a heterochromatin-rich chromosome configuration, that might have been involved in diversification of this genus. Vigna umbellata, which is domesticated extensively in the sub tropical hilly and moist regions of North-east India, had its heterochromatin blocks rich in AT content with fewer GC base pairs. On the contrary, more GC content in heterochromatin blocks was observed in V. aconitifolia, which is acclimatized to the arid and semi-arid region of tropical Western plains of India, helping the species to overcome adverse climatic conditions of Indian desert. Our observations in this regard constitute a first attempt to probe the role of heterochromatin distribution pattern, if any, in species differentiation of plant groups.

Acknowledgements

The present work is supported by a grant from the World Bank funded by Indian Council of Agriculture Research (ICAR) project received through National Agriculture Innovation Program (NAIP). We thank the Head, Department of Biotechnology and Bioinformatics, North Eastern Hill University (NEHU), Shillong for providing facilities. Sincere thanks are also due to members of the Plant Biotechnology Laboratory for their help. The generous support for germplasm of V. umbellata extended by Dr. A. Pattanayak, Division of Biotechnology, ICAR complex for North Eastern Hill Region, Barapani, Meghalaya is duly acknowledged.

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