ISRN Genetics

Volume 2013 (2013), Article ID 651019, 6 pages

http://dx.doi.org/10.5402/2013/651019

Research Article

Genetic Divergence in Indigenous Wild and Cultivated Rice Species of Manipur Valley

K. Medhabati,¹ K. Rajiv Das,² M. Rohinikumar,³ H. Sunitibala,¹ and Th. Dikash Singh¹

¹Medicinal Plant and Horticulture Division, Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795001, India

²Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli 620024, India

³Director of Research, Central Agricultural University, Iroisemba, Imphal 795004, India

Received 25 August 2012; Accepted 19 September 2012

Academic Editors: J. Huang and D. Sun

Copyright © 2013 K. Medhabati et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract.

Genetic divergence of 32 indigenous rice germplasms and five wild rice of which three from Manipur and two wild rice procured from IRRI, Philippines was investigated using Mahalanobis, statistic. Based on twelve agromorphological characters, the thirty-seven germplasms both wild and cultivated were grouped into five clusters based on the relative magnitudes of values following Tocher's method of cluster formation. Based on the rank totals, the characters which contributed maximum towards genetic divergence in the present studies were grain yield/plant, spikelet/panicle, 100 grain weight, grain length, days to 50% flowering, ear bearing tillers/plant, and flag leaf length. In the present study, maximum intercluster distance was estimated between cluster III and () which was closed followed by clusters II and V (). On the basis of their greater intercluster distance, high value of cluster mean according to the character to be improved and performance of the individual germplasms for the character, the germplasms could be used in hybridization programme for improvement of different plant characters in the rice germplasms of Manipur.

1. Introduction

Manipur valley which is also considered as rice bowl of the state has a large variability of indigenous rice cultivars that belong to Asian cultivated rice O. sativa L. subspecies indica. So far, 44 indigenous rice cultivars along with two wild rice wainuchara one with perennial form and murshi another with annual weedy form have been recorded from Manipur valley by Singh and Sharma [1]. If one considers the percentage availability of indigenous rice cultivar per unit area Manipur valley has one land race of rice per 42 sq·km. According to traditional classification, more than 50 rice cultivars were cultivated in Manipur valley before the introduction of high-yielding varieties bred in Manipur. The high-yielding varieties of rice introduced from the plain or hill regions of the northern and southern parts of the country do not perform well in northeastern hill region [2]. The importance of local land races of rice in breeding programme lies in the evolution of gene complexes in the local cultivars that have coadapted to specific local environment through long period of natural selection. These gene complexes may not be readily reconstituted even by the modern recombinant DNA technology; we have to utilize the naturally occurring gene complexes for breeding of rice for specific local conditions.

The basic importance of genetic diversity in breeding for high yield has long been recognized as is evident from the results reported by several workers in different crops. The magnitude of heterosis in crop plants depends on the degree of genetic divergence between parental stocks and, consequently, may be used as an indicator of the inherent yielding capacity of a cross. While the importance of genetic diversity has long been appreciated by breeders, the basic difficulty has always been one of recognizing and estimating such diversity, shortness of actually making the cross. In view of the great importance of genetic diversity to breeding, techniques which can provide direct and reliable quantitative estimates of diversity at the genotypic level should prove to be valuable. In crop improvement programme, the importance of genetic diversity existing in the material has been emphasized by several workers [3, 4]. The more diverse the parents, the more are the chances of increased spectrum of variability. Systematic evaluations of local rice germplasms of both O. sativa cultivars and wild species for morphological and agronomic characters and genetic diversity are urgently needed as far as the improvement of the local germplasms are contemplated. Such a study should also allow critical evaluation of the adaptive radiation of rice cultivars, for crop plants evolved from wild species in the areas showing great genetic diversity followed by a ramification of an adaptive type in a series of new adaptive zones [5]. The wealth of Manipur in terms of local rice germplasms is threatened by the rapid spread of newly developed improved rice varieties. Old and obscure rice varieties are being rapidly replaced by new ones in many areas. Primitive and wild forms are being wiped out by land clearing associated with irrigation and drainage projects, housing and urbanization, and so forth. For several decades, it was taken for granted that diverse rice germplasms were readily available in the native habitats of the crop. However, the gradual and widespread disappearance of the diverse and less productive indigenous land races by replacement with improved cultivars went on unnoticed. It is in this context that scientists, particularly the plant breeders of the state started giving their thought with all seriousness for the conservation of local rice germplasms. Thus, it is extremely important to study the genetic composition of the germplasms of existing modern day cultivars in comparison with their ancestors and related species. This will not only provide information on their phylogenetic relationship but also will indicate a chance of finding new and useful genes, as the accessions with most distinct DNA profiles are likely to contain a greater number of novel alleles.

The use of Mahalanobis statistics for estimating genetic divergence had been emphasized by many workers [4–7] because it permitted precise comparison among all possible pairs of population in any group before affecting actual crosses. In addition to aiding in the selection of divergent parents for hybridization, statistics measures the degree of diversification and determines the relative contribution of each component character to the total divergence [8]. The utility of multivariate analysis in quantifying the degree of divergence between populations to understand the trend of evolutionary pattern, to assess the relative contribution of different components to the total divergence and to determine the nature of forces operating on inter- and intra-cluster levels has greatly been emphasized [9–12]. Further, such studies have also permitted the choice of genetically divergent parents to obtain desirable recombinants in segregating generations [13].

2. Materials and Methods

The experimental material consisted of 35 indigenous rice germplasms of Manipur valley, namely, Thoubal district with 15 germplasms, Imphal district with 10 germplasms and Bishenpur district with 10 germplasms, and 2 wild rice O. rufipogon and O. nivara procured from IRRI, Philippines, 3 wild rice from Manipur valley, namely, O. rufipogon local cultivars namely wainuchara, wainuchara manbi, and murshi. Accession numbers and local names of the germplasms are given in Table 1.

Table 1: Name of the genotypes included in the experiment.

Sl. no.
Acc no.
Local name of the cultivars
Place of collection/parentage

1
31
Chak-hao amubi
Thoubal district

2
32
Chak-hao angouba
Imphal district

3
33
Chak-hao poireiton
Imphal district

4
34
Chak-hao sempak
Imphal district

5
40
Champra phou
Imphal district

6
47
Changlei
Thoubal district

7
70
Heitup phou
Thoubal district

8
74
Iroya
Thoubal district

9
74A
Iroya A
Thoubal district

10
84
Kakcheng phou
Bishenpur district

11
119
Kumbi phou
Bishenpur district

12
123
Laiphou
Thoubal district

13
129
Langmanbi
Thoubal district

14
130
Langphou
Bishenpur district

15
166
Moirangphou
Bishenpur district

16
167
Moirangphou khokngangbi
Bishenpur district

17
167A
Moirangphou khokngangbi A
Bishenpur district

18
195
Phoudum
Imphal district

19
196
Phougak
Thoubal district

20
197
Phoungang
Bishenpur district

21
198
Phourel
Thoubal district

22
199
Phourel akuppi
Thoubal district

23
200
Phourel amubi
Thoubal district

24
201
Phourel noining
Imphal district

25
202
Phourel phoudongba
Imphal district

26
203
Phourel phoujao
Thoubal District

27
204
Phourel tujombi
Thoubal district

28
218
Sangsangba
Imphal district

29
236
Taothabi
Bishenpur district

30
237
Taothabi angouba
Bishenpur district

31
255
Tumai angouba
Imphal district

32
263
Phourel yenthik
Bishenpur district

Name of the wild cultivars

33
1
O. rufipogon local cultivar 1 wainuchara
Bishenpur district

34
2
O. rufipogon local cultivar 2 wainuchara manbi
Bishenpur district

35
3
O. rufipogon local cultivar 3 murshi
Imphal district

36
4
Oryza rufipogon
IRRI, Philippines

37
5
Oryza nivara
IRRI, Philippines

These germplasms were grown in the experimental farm of Manipur University, Manipur, India during kharif season of 2009 and 2010. The experiment was laid out in the research field of the University in the randomized block design with three replications. The interrow spacing was maintained at 20 cm. The recommended plant protection measures and agronomical practices were followed. The experimental data on various quantitative and qualitative characters were recorded as per criteria laid down in the standard Evaluation System for rice IRTP and “Descriptors for Rice” published jointly by International Rice Research Institute and International Board for plant Genetic Resources [14]. Ten plants from middle three rows of each plot were randomly sampled and the quantitative characters were recorded following actual measurement on each of the sampled plants and then averaged it out. The qualitative traits were recorded through visual observation only. Nine qualitative traits were taken for the study. They are leaf blade colour, leaf blade pubescence, basal leaf sheath colour, leaf angle, ligule colour, collar colour, auricle colour, flag leaf angle, and ligule shape. The variables measured for quantitative characters were flag leaf length, flag leaf width, ligule length, culm diameter, panicle length, culm length, ear bearing tillers/plant, days to 50% flowering, grain length, 100 grain weight, spikelet/panicle, and grain yield/plant. The two-year data were pooled in the analysis. Mahalanobis statistics was used to estimate genetic divergence among the thirty-seven germplasms. The germplasms were grouped into clusters according to Tocher’s methods by Rao [15].

3. Results and Discussion

The thirty-seven rice germplasms both wild and cultivated were grouped into five clusters based on the relative magnitude of values following the Tocher’s method of cluster formation [15] with the criterion that the intracluster average values should be less than the intercluster values (Table 2). Maximum cultivars were in cluster I involving 25 out of 37 germplasms (Table 3). However, clusters IV and V had only one cultivar each. Average inter- and intra-cluster distances are presented in cluster diagram (Figure 1) and are also presented as a supplement of the table using values of average inter- and intra-cluster. This depicted the genetic diversity in an easily understandable manner and provided information about relationships of different clusters. But the diagram presented was not exactly to the scale. The value of intracluster distance ranged from 0.00 (clusters IV and V) to 5.98 (cluster 1). It could be indicated that clusters I and III were highly divergent from clusters II, IV, and V. Moreover, cluster IV appeared less divergent from cluster II and cluster V to cluster III based on the values of intracluster distances. The average intercluster distance varied from 44.78 (clusters V and II) to 198.44 (clusters III and II). From the intercluster distances, it could be inferred that the cultivars belonging to clusters III and II (198.44) and clusters V and II (156.32) were more divergent and had a wide genetic variation than the others.

Table 2: Average intra- and inter-cluster and values of 37 rice cultivars of Manipur Valley.

I
II
III
IV
V

I
35.80
63.89
114.69
55.13
109.69

(5.98)
(9.99)
(10.71)
(7.42)
(10.47)

II

34.18
198.44
90.65
156.32

(5.35)
(14.09)
(9.52)
(12.50)

III

36.15
70.70
44.78

(6.01)
(8.41)
(6.69)

IV

0.0
54.27

(7.37)

V

0.0

Table 3: Grouping of 37 rice cultivars into 5 clusters.

Cluster
No. of cultivars included
Name of cultivar with entry no.

I
25
Chak-hao angouba (32), Chak-hao poireiton (33), Chakhao-sempak (34), Heitup phou (70), Iroya (74), Kakcheng phou (84), Langmanbi (129), Moirangphou khokngangbi (167), Phourel phoudongba (202), Phourel phoujao (203), Changlei (47), Kumbi-phou (119), Laiphou (123), Sangsangba (218), Taothabi (236), Langphou (130), Moirangphou (166), Chak-hao amubi (31), Champra phou (40), Phoudum (195), Phourel yenthik (263), Tumai angouba (255), Phourel tujombi (204), Moirangphou khokngangbi (A), and Phougak (196)

II
6
Iroya A (74A), Phoungang (197), Phouren (198), Phourel akupi (199), Phouren amubi (200), and Phouren noining (201)

III
4
Oryza wainuchara, syn. O. rufipogon, local collection 11 (1), Oryza wainucharamanbi, syn. O. rufipogon local collection 111 (2), Oryza murshi, syn. O. rufipogon, local collection 1 (3), and Oryza rufipogon (4)

IV
1
Taothabi angouba (237)

V
1
O. nivara (5)

Figure 1: Cluster diagram with inter- and intra-cluster distance ().

Clustering of thirty-seven germplasms with twenty-five germplasms into cluster I, six germplasms in cluster II, four germplasms in cluster III, and one germplasms each in clusters IV and V, each indicated presence of genetic diversity among the germplasms (Table 3). The random clustering pattern of germplasms from different valley districts of Manipur indicated that the genetic diversity of the germplasms is not necessarily related with the distribution of germplasms in different districts of Manipur valley. The genetic diversity among the germplasms in the present study may be resulted from genetic drift and selection that cause greater diversity than geographical distribution of Manipur valley as suggested by Murty and Arunachalan [4]. Taothabi angouba and Oryza nivara maintained their separate identities by making monogenetic groups, that is, clusters IV and V while forming clusters. It might be due to its different genetic makeup from that of the other germplasms.

3.1. Average Inter- and Intra-Cluster Distances

Maximum intercluster distance suggested wider diversity between the groups; while minimum intercluster distance indicated closer relationship by Singh et al. [16]. Higher intracluster distance also indicated greater heterogeneity of the cultivars by Pattnaik [17]. Genotypes belonging to different clusters separated by high estimated statistical distance could be used in hybridization programme for obtaining a wide spectrum of variation among the segregants [18]. Further, the magnitude of heterosis largely depends upon the degree of genetic diversity in the parental lines Roy and Panwar [19].

In the present study, maximum intercluster distance was estimated between cluster III (), which was closely followed by cluster II, and V (). It is suggested that the crossing between the selected germplasms from clusters II and III or clusters II and V will give rise to high heterotic crosses and a wide spectrum of variation among the segregants. Since cluster 1 consisted of 25 germplasms with appreciably high value of intracluster distances, presence of high heterogeneity among the germplasms is expected. Hence, subclustering of cluster 1 is an approach towards the effective selection of desired parents for hybridisation programme within the cluster. The maximum inter-sub-clusters III and V which was closely followed by subclusters VIII and IX.

3.2. Diversity in 12 Agronomic Characters

Diversity in 12 agronomic characters of rice germplasms was shown in Table 4. Considerable genetic diversity is observed in almost all the characters of the cultivars under study.

Table 4: Diversity in 12 agronomic characters of 37 rice germplasms.

S. no.
Characters
Minimum
Maximum

1
Flag leaf length
19.44 O. rufipogon local cultivar (2) wainuchara manbi
51.19 Phourel amubi (200)

2
Flag leaf width
0.97 O. rufipogon local cultivar (3) murshi
1.84 Champra phou (40)

3
Ligule length
1.22 Chak-hao poireiton (33)
3.06 Chak-hao poireiton (33)

4
Culm diameter
0.60 Langphou (130)
1.42 Phourel (198)

5
Panicle length
19.42 Chak-hao amubi (31)
27.56 Heitup phou (70)

6
Culm length
73.87 O. rufipogon local cultivar (1) wainuchara
159.00 Phougak (196)

7
Ear bearing tillers/plant
5.50 O. rufipogon local cultivar (1) wainuchara
13.67 Phourel akupi (199)

8
Days to 50% flowering
87.33 Phoudum (195)
121.17 Phourel (198)

9
Grain length
0.77 Phoudum (195)
2.36 Chak-hao poireiton (33)

10
100 grain weight
1.85 Oryza rufipogon (4)
3.80 Chak-hao poireiton (33)

11
Spikelet number/panicle
56.67 Oryza rufipogon (4)
151.73 Phoungang (197)

12
Grain yield/plant
5.22 O. rufipogon Local cultivar (3) murshi
44.95 Phourel (198)

3.3. Analysis

The calculated values of were tested against the tabulated values of at 5% level of significance for 12 degrees of freedom being much lower than minimum calculated values of which obviously shows that values were significant.

3.4. Contribution of Each Germplasm towards Divergence

The relative contribution of each germplasm towards divergence is presented in Table 5. It was revealed from the table that germplasm O. rufipogon had an average maximum value of divergence () closely followed by Oryza murshi (), wainuchara manbi (), O. nivara (), Phouren (), and O. rufipogon local cultivar 1 wainuchara () and in divergence () closely followed by O. rufipogon local cultivar 3 murshi (), O. rufipogon local cultivar 2 wainuchara manbi (), O. nivara (), Phouren (), and O. rufipogon local cultivar 1 wainuchara () and in turn contributed 5.76%, 5.13%, 5.07%, 4.51%, 4.24%, 3.77%, respectively, towards total divergence. On the other hand, germplasm Laiphou had minimum average divergence () which contributed only 1.20% towards divergence and followed by Changlei (), Phourel phoujao (), and Kumbi phou () contributing 1.73%, 1.73%, and 1.78%, respectively, towards divergence. It may, further, be pointed out that the remaining germplasms had an average value ranging from 43.31 to 102.16 and contributed only from 1.80% to 4.24% towards divergence.

Table 5: Relative contributions of individual character towards divergence calculated under different methods.

Sl. no.
Characters
Rank total
Percentage to rank total

1
Flag leaf length
1763
3.40

2
Flag leaf
3586
6.90

3
Ligule length
6841
13.17

4
Culm diameter
18093
34.82

5
Panicle length
6321
12.17

6
Culm length
4954
9.54

7
Ear bearing tillers/plant
1961
3.77

8
Days to 50% flowering
2831
5.45

9
Grain length
2465
4.7

10
100 grain weight
1031
1.98

NB: In this method, the smallest contribution to the percentage rank total will be the highest contribution towards divergence. It is just opposite to other methods. This means that if the rank total increases, the percentage of contribution towards divergence decreases.

The present findings indicated that, maximum intercluster distance was estimated between cluster III () which was closely followed by clusters II and V (). It is s suggested that the crossing between the selected germplasms from clusters II and III or clusters II and V will give rise to high heterotic crosses and a wide spectrum of variation among the segregants. However, hybridization programme between the germplasms of cluster I, if considered necessary, crossing between the selected germplasms from the subcluster III and V or VIII and VII or III and VIII or III and VI is expected to give the satisfactory result.

The salient findings obtained from the present studies and their possible implications in the genetic improvement of indigenous and wild rice germplasms of Manipur are summarised hereunder. In the studies for genetic divergence of 37 rice germplasms, significance of values revealed the presence of considerable divergence among the genotypes. Based on the rank totals, the characters which contributed maximum towards genetic divergence in the present studies were grain yield/plant, spikelets/panicle, 100 grain weight, grain length, days to 50% flowering, ear bearing tillers/plant, and flag leaf length. Clusters with the highest mean values of agronomic characters and best-performing germplasms within the cluster were identified. Best performers for hybridisation were shown in Table 6.

Table 6: Best performers for hybridization.

Sl. no.
Germplasms
Characters

1
Phourel amubi
Flag leaf length

2
Chak-hao Poireiton

and Champra phou
Flag leaf width

3
Phouren

4
Chak-hao poireiton

5
Heitup phou

6
Phougak
Culm length

7
Phouren akuppi
Ear bearing tillers/plant

8
Phoungang
Spikelet number/plant

4. Conclusion

Rice being the staple food crop of the people of Manipur, rice culture itself was associated with the history and culture of Manipur. As the state of Manipur is located in the Indo-China region, which is considered to be the primary centre of origin of rice, diverse forms of indigenous rice cultivars or land races including the wild forms are expected. The expectations of the presence of wild rice and diverse forms of wild rice O. rufipogon local cultivar 1 “wainuchara” and annual weedy rice O. rufipogon local cultivar 3 “murshi” and one land race per 42 sq·km area of Manipur valley. The future scope of the present investigation is to go further into the research and development work for improvement of indigenous rice germplasms of Manipur valley. Based on the present findings, breeding for various objectives in the indigenous rice cultivars of Manipur valley to be continued. Gene actions for various quantitative traits in the selected parents are to be investigated in order to adopt appropriate breeding techniques for production breeding programmes of local rice germplasms of Manipur. The above observations open up a new vista to the rice researchers of Manipur to obtain a first-hand information regarding variability of rice germplasms and also to trace the phylogenetic relationship between the indigenous rice varieties and their wild progenitors through analysis.

Conflict of Interests

The authors declare that they have no conflict of interests.

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