Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India

doi:10.1016/S1672-6308(14)60287-0

Abstract

Abstract:

A set of 50 rice genotypes comprising landraces, local selections, and improved varieties were characterized using simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers to study genetic diversity and population structure. Following unweighted pair group method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 5 clusters and 11 sub-clusters, whereas population structure analysis separated 50 rice genotypes into 5 sub-populations. Grouping of rice genotypes showed better resemblance with the pedigree information of the genotypes. Both genetic diversity and population structure analysis separated majority of the improved varieties from landraces and local selections. Some of the SSR markers amplified unique alleles which were specific to a particular genotype and could distinguish them from the rest. The results indicate that these rice genotypes exhibit a higher genetic diversity and can be very useful in rice improvement program.

Key words: rice, genetic diversity, molecular marker, population structure, simple sequence repeat

D. Kumbhar Shailesh, L. Kulwal Pawan, V. Patil Jagannath, D. Sarawate Chandrakant, P. Gaikwad Anil, S. Jadhav Ashok. Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India[J]. Rice Science, 2015, 22(3): 99-107.

Figures/Tables 6

References 30

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Genotype	Parentage/detail
Heera	CR404-48 × CR289-1208
Halvi Sal 17	Local selection from Kolhapur (MS)
RDN185-2	Halvi Sal 17 × TN1
Phule Radha	TN1 × Kolamba 540
RTN1	IR8 × RTN24
Ratna	TKM6 × IR8
Phule Samruddhi	Indrayani × Sonsali
Jaya	TN1 × T141
Phule Maval	Pawana × Indrayani
Pawana	Pusa 33 × IR28
Indrayani	Ambemohar 157 × IR8
Bhogavati	Selection from Basmati composite
Pusa Basmati 1	Pusa 150 × Karnal Local
Ghansal	Local selection from Kolhapur (MS)
Kalajirga	Local selection from Kolhapur (MS)
Vivek Dhan 82	VL221 × UPR82-1-7
Badshabhog	Local type/landrace from Orissa
Kothimbire	Landrace from Kolhapur (MS)
BPT5204	(GEB24 × TN1) × Mahsuri
RDN98-2-3-5-14	Halvi Sal 17 × TN1
RDN01-2-10-9	Ambemohar 157 × IR8
KJT2	RP6-17 × RP4-14
EK70	Landrace from Igatpuri, Nasik (MS)
Patni	Landrace from Sindhudurg (MS)
Diwani	Landrace from Uttar Pradesh
Shyam Jeer	Landrace from Bihar
Kasturi	Basmati 370 × CRR88-17-1-5
SD17	Pusa Basmati 1 × IET12603
Sugandhamati	Pusa Basmati 1 × IET12603
Basmati 386	Selection from Pak Basmati
MC4	Selection from Karnal Local
Haryana Basmati	Local selection from Haryana
Mahisugandha	BK79 × Basmati 370
Khalibagh	Landrace from Sindhudurg (MS)
Vikram	Landrace from Sindhudurg (MS)
Tulshi tall	Landrace from Kolhapur (MS)
Champakali	Landrace from Kolhapur (MS)
Siddhagiri	Landrace from Kolhapur (MS)
RDN97-2	TN1 × IR64
RDN99-12	Selection from Phule Maval
RDN99-14	Bhogavati × RTN24
RTN purple	Local selection from Ratnagiri (MS)
Taraori Basmati	Pureline selection from NBC19
RDN02-80	Indrayani × Pusa Basmati 1
Pavsal	Landrace from Pune (MS)
Antersal	Landrace from Pune (MS)
Nalabhat	Landrace from Pune (MS)
Sonsali	Landrace from Pune (MS)
LK248	Local selection from Nasik (MS)
Pomendi Local	Landrace from Ratnagiri (MS)

Genotype	Parentage/detail
Heera	CR404-48 × CR289-1208
Halvi Sal 17	Local selection from Kolhapur (MS)
RDN185-2	Halvi Sal 17 × TN1
Phule Radha	TN1 × Kolamba 540
RTN1	IR8 × RTN24
Ratna	TKM6 × IR8
Phule Samruddhi	Indrayani × Sonsali
Jaya	TN1 × T141
Phule Maval	Pawana × Indrayani
Pawana	Pusa 33 × IR28
Indrayani	Ambemohar 157 × IR8
Bhogavati	Selection from Basmati composite
Pusa Basmati 1	Pusa 150 × Karnal Local
Ghansal	Local selection from Kolhapur (MS)
Kalajirga	Local selection from Kolhapur (MS)
Vivek Dhan 82	VL221 × UPR82-1-7
Badshabhog	Local type/landrace from Orissa
Kothimbire	Landrace from Kolhapur (MS)
BPT5204	(GEB24 × TN1) × Mahsuri
RDN98-2-3-5-14	Halvi Sal 17 × TN1
RDN01-2-10-9	Ambemohar 157 × IR8
KJT2	RP6-17 × RP4-14
EK70	Landrace from Igatpuri, Nasik (MS)
Patni	Landrace from Sindhudurg (MS)
Diwani	Landrace from Uttar Pradesh
Shyam Jeer	Landrace from Bihar
Kasturi	Basmati 370 × CRR88-17-1-5
SD17	Pusa Basmati 1 × IET12603
Sugandhamati	Pusa Basmati 1 × IET12603
Basmati 386	Selection from Pak Basmati
MC4	Selection from Karnal Local
Haryana Basmati	Local selection from Haryana
Mahisugandha	BK79 × Basmati 370
Khalibagh	Landrace from Sindhudurg (MS)
Vikram	Landrace from Sindhudurg (MS)
Tulshi tall	Landrace from Kolhapur (MS)
Champakali	Landrace from Kolhapur (MS)
Siddhagiri	Landrace from Kolhapur (MS)
RDN97-2	TN1 × IR64
RDN99-12	Selection from Phule Maval
RDN99-14	Bhogavati × RTN24
RTN purple	Local selection from Ratnagiri (MS)
Taraori Basmati	Pureline selection from NBC19
RDN02-80	Indrayani × Pusa Basmati 1
Pavsal	Landrace from Pune (MS)
Antersal	Landrace from Pune (MS)
Nalabhat	Landrace from Pune (MS)
Sonsali	Landrace from Pune (MS)
LK248	Local selection from Nasik (MS)
Pomendi Local	Landrace from Ratnagiri (MS)

Marker	Total no. of alleles	No. of monomorphic alleles	No. of unique alleles	Polymorphism (%)	PIC
RM11	2	0	0	100	0.461
RM21	3	0	0	100	0.663
RM44	20	0	0	100	0.91
RM72	5	0	0	100	0.765
RM162	9	0	1	100	0.765
RM204	23	0	2	100	0.928
RM209	8	0	0	100	0.811
RM215	5	0	1	100	0.607
RM224	15	0	1	100	0.901
RM241	17	0	2	100	0.923
RM246	22	0	0	100	0.917
RM259	20	0	0	100	0.963
RM307	4	0	0	100	0.523
TRS26	15	0	0	100	0.893
TRS33	19	0	2	100	0.902
ISSR808	3	1	0	66.7	0.105
ISSR809	9	0	0	100	0.818
ISSR810	10	0	0	100	0.867
ISSR811	9	0	0	100	0.866
ISSR812	10	1	0	90	0.85
ISSR813	8	0	0	100	0.851
ISSR814	4	0	0	100	0.65
ISSR815	12	0	0	100	0.91
ISSR818	6	0	0	100	0.648
ISSR821	6	0	0	100	0.793
ISSR823	12	1	0	91.7	0.913
ISSR826	3	0	0	100	0.197
ISSR827	11	0	0	100	0.989

Marker	Total no. of alleles	No. of monomorphic alleles	No. of unique alleles	Polymorphism (%)	PIC
RM11	2	0	0	100	0.461
RM21	3	0	0	100	0.663
RM44	20	0	0	100	0.91
RM72	5	0	0	100	0.765
RM162	9	0	1	100	0.765
RM204	23	0	2	100	0.928
RM209	8	0	0	100	0.811
RM215	5	0	1	100	0.607
RM224	15	0	1	100	0.901
RM241	17	0	2	100	0.923
RM246	22	0	0	100	0.917
RM259	20	0	0	100	0.963
RM307	4	0	0	100	0.523
TRS26	15	0	0	100	0.893
TRS33	19	0	2	100	0.902
ISSR808	3	1	0	66.7	0.105
ISSR809	9	0	0	100	0.818
ISSR810	10	0	0	100	0.867
ISSR811	9	0	0	100	0.866
ISSR812	10	1	0	90	0.85
ISSR813	8	0	0	100	0.851
ISSR814	4	0	0	100	0.65
ISSR815	12	0	0	100	0.91
ISSR818	6	0	0	100	0.648
ISSR821	6	0	0	100	0.793
ISSR823	12	1	0	91.7	0.913
ISSR826	3	0	0	100	0.197
ISSR827	11	0	0	100	0.989

Cluster	Sub-cluster	No. of genotypes	Genotype	Remark
I	A	4	Heera, SD17, Sugandhamati, MC4	Basmati line Karnal Local as parent or in ancestry, except Heera
I	B	1	RDN02-80	Basmati line Karnal Local as parent or in ancestry, except Heera
II	A	7	Halvi Sal 17, EK70, Patni, Siddhagiri, RDN97-2, Khalibagh, Sonsali	Non-scented, landraces or local selections, except RDN97-2
II	B	3	Kalajirga, Kasturi, Champakali	Scented landraces except Kasturi
III	A	14	RDN185-2, Phule Radha, RTN1, Pawana, Jaya, Ratna, Phule Samruddhi, Phule Maval, Indrayani, Bhogavati, RDN01-2-10-9, KJT2, BPT5204, RDN98-2-3-5-14	All improved varieties with dwarf plant type, IR8 or TN1 as parent or in ancestry
	B	5	RDN99-12, RDN99-14, RTN purple, LK248, Pomendi Local	Dwarf plant type, midlate to late maturity, medium slender grain type
	C	2	Nalabhat, Taroari Basmati	Landraces, long-slender grain type, late maturity
	D	3	Vivek Dhan 82, Haryana Basmati, Antersal	Tall plant type
IV		2	Vikram, Tulshi tall	Landraces
V	A	4	Pusa Basmati 1, Ghansal, Badshabhog, Pavsal	Scented Basmati or non-Basmati genotypes; mostly landraces
	B	5	Kothimbire, Diwani, Shyam Jeer,	Scented Basmati or non-Basmati genotypes; mostly landraces
	B	5	Basmati 386, Mahisugandha	Scented Basmati or non-Basmati genotypes; mostly landraces