Genetic diversity of coconut germplasm native to South Kalimantan, Indonesia: a molecular study

Mursyidin, Dindin Hidayatul; Ahyar, Gusti Muhammad Zainal

doi:10.1590/1983-40632022v5271016

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Research Article • Pesq. Agropec. Trop. 52 • 2022 • https://doi.org/10.1590/1983-40632022v5271016 copy

Genetic diversity of coconut germplasm native to South Kalimantan, Indonesia: a molecular study

Diversidade genética de germoplasma de coco nativo de Kalimantan do Sul, Indonésia: um estudo molecular

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

Coconut (Cocos nucifera L.) is one of the most important tree crops in the world, especially in the tropics. This study aimed to determine the genetic diversity of coconut germplasm native to South Kalimantan, Indonesia, using the rbcL marker. Nine coconut samples, being eight natively collected from this region and one as an outgroup (obtained from the GenBank database), were used in the study. According to the rbcL marker, the coconut germplasm native to South Kalimantan has a relatively high diversity, with a nucleotide diversity (π) of 0.51. The level of diversity is strongly correlated with the mutation present in the observed region, rbcL. The phylogenetic analysis showed that the coconut germplasm has a unique relationship, where the ‘Dalam’ cultivar is the closest to three other dwarf coconuts, i.e., ‘Genjah Kuning 1’, ‘Genjah Kuning 3’ and ‘Wulung’.

KEYWORDS:
Cocos nucifera L; breeding program; phylogenetic analysis

Coconut samples	Type	Origin
‘Dalam’	Tall	Barito Kuala, South Kalimantan
‘Genjah Kuning 1’	Dwarf	Banjarbaru, South Kalimantan
‘Genjah Kuning 2’^* * Introduction;	Dwarf	Barito Kuala, South Kalimantan
‘Genjah Kuning 3’	Dwarf	Tanah Laut, South Kalimantan
‘Genjah Salak 1’	Dwarf	Banjarbaru, South Kalimantan
‘Genjah Salak 2’	Dwarf	Banjar, South Kalimantan
‘Genjah Salak 3’^* * Introduction;	Dwarf	Barito Kuala, South Kalimantan
‘Genjah Wulung’	Dwarf	Barito Kuala, South Kalimantan
Voucher 2153^ outgroup obtained from the GenBank (accession number KX587647).	Dwarf	Puerto Rico

Parameter	Information
Nucleotide diversity (π)	0.51
Number of segregation sites (S)	577
Transition/transversion bias value (R)	0.66
Guanine-Cytosine (GC) content (%)	42.93
Tajima neutrality test (D)	2.42
Bayesian information criterion (BIC)	8,111.01
Akaike information criterion (AICc)	8,006.41
Maximum likelihood value (lnL)	-3,987.15

Operational taxonomic units	Code	A	B	C	D	E	F	G	H	I
‘Dalam’	A	0.00
‘Genjah Kuning 1’	B	0.00^a a very closely related;	0.00
‘Genjah Kuning 2’	C	3.48	3.48	0.00
‘Genjah Kuning 3’	D	0.00^a a very closely related;	0.00^a a very closely related;	3.44	0.00
‘Genjah Salak 1’	E	2.98	2.98	4.87	3.03	0.00
‘Genjah Salak 2’	F	3.63	3.63	4.41	3.59	4.44	0.00
‘Genjah Salak 3’	G	2.92	2.92	5.07^b b farthest related.	2.97	0.01	4.61	0.00
‘Genjah Wulung’	H	0.00^a a very closely related;	0.00^a a very closely related;	3.48	0.00^a a very closely related;	2.98	3.63	2.92	0.00
Voucher 2153^* * Outgroup;	I	3.44	3.44	3.83	3.46	4.12	3.90	3.94	3.44	0.00

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[TFN1] ^*
Introduction;

[TFN2] ^**
outgroup obtained from the GenBank (accession number KX587647).