How to develop population structure from ssr marker?
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Using SSR markers to map genetic diversity
and population structure of Solanum
pimpinellifolium for development of a core
collection
Eguru Sreenivasa Rao
†
, Palchamy Kadirvel
‡
, Rachael C. Symonds,
Subramaniam Geethanjali
§
and Andreas W. Ebert*
AVRDC – The World Vegetable Center, PO Box 42, Shanhua, Tainan 74199, Taiwan,
Republic of China
Received 16 September 2011; Accepted 17 November 2011 – First published online 12 December 2011
Abstract
The present study was undertaken to examine the population structure of the Solanum
pimpinellifolium collection maintained by AVRDC – The World Vegetable Center – and to
construct a core set of this collection. Out of the entire collection of 322 accessions, a diverse
subset of 190 accessions was chosen representing 14 countries of origin. Data on 32 qualitative
and 22 quantitative phenotypic traits (IPGRI–AVRDC descriptor traits) and 48 simple sequence
repeat markers evenly distributed over the genome were used to develop the core set. A total
of 377 alleles were detected with 7.85 alleles per locus, on average. Of these, 52 alleles at
28 loci were extremely rare-frequency alleles. The 190 accessions clustered into two main
populations and an admixture group. Population I (PopI) included 99 accessions, 93 of
which originated from Peru. Population II (PopII) contained 49 accessions, the majority of
which originated from Ecuador and Mexico. The remaining 42 accessions were classified as
admixture group. The two main populations were further subdivided into five subgroups.
Values of F
st
among the five sub-populations were significant (average pairwise F
st
of 0.296),
suggesting a real difference between these populations. A clear differentiation was observed
among and within populations based on geography. Peruvian accessions were genetically
more diverse than accessions originating in Ecuador and Mexico. Within the Peruvian group,
a gradual increase in genetic diversity was observed from southern to northern Peru. The
constructed core collection consists of 75 accessions representing 23.4% of AVRDC’s entire
S. pimpinellifolium collection and 39.5% of the subset used in this study. It is a well-balanced
core with a good representation of the different populations (31 accessions from PopI,
22 from PopII and 22 from the Admixture group) and geographic origins (40 accessions from
Peru, 17 from Ecuador, 14 from
and population structure of Solanum
pimpinellifolium for development of a core
collection
Eguru Sreenivasa Rao
†
, Palchamy Kadirvel
‡
, Rachael C. Symonds,
Subramaniam Geethanjali
§
and Andreas W. Ebert*
AVRDC – The World Vegetable Center, PO Box 42, Shanhua, Tainan 74199, Taiwan,
Republic of China
Received 16 September 2011; Accepted 17 November 2011 – First published online 12 December 2011
Abstract
The present study was undertaken to examine the population structure of the Solanum
pimpinellifolium collection maintained by AVRDC – The World Vegetable Center – and to
construct a core set of this collection. Out of the entire collection of 322 accessions, a diverse
subset of 190 accessions was chosen representing 14 countries of origin. Data on 32 qualitative
and 22 quantitative phenotypic traits (IPGRI–AVRDC descriptor traits) and 48 simple sequence
repeat markers evenly distributed over the genome were used to develop the core set. A total
of 377 alleles were detected with 7.85 alleles per locus, on average. Of these, 52 alleles at
28 loci were extremely rare-frequency alleles. The 190 accessions clustered into two main
populations and an admixture group. Population I (PopI) included 99 accessions, 93 of
which originated from Peru. Population II (PopII) contained 49 accessions, the majority of
which originated from Ecuador and Mexico. The remaining 42 accessions were classified as
admixture group. The two main populations were further subdivided into five subgroups.
Values of F
st
among the five sub-populations were significant (average pairwise F
st
of 0.296),
suggesting a real difference between these populations. A clear differentiation was observed
among and within populations based on geography. Peruvian accessions were genetically
more diverse than accessions originating in Ecuador and Mexico. Within the Peruvian group,
a gradual increase in genetic diversity was observed from southern to northern Peru. The
constructed core collection consists of 75 accessions representing 23.4% of AVRDC’s entire
S. pimpinellifolium collection and 39.5% of the subset used in this study. It is a well-balanced
core with a good representation of the different populations (31 accessions from PopI,
22 from PopII and 22 from the Admixture group) and geographic origins (40 accessions from
Peru, 17 from Ecuador, 14 from
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