Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo

Thomson, Michael J.; Polato, Nicholas R.; Prasetiyono, Joko; Trijatmiko, Kurniawan Rudi; Silitonga, Tiur S.; McCouch, Susan R.

doi:10.1007/s12284-009-9023-1

Cited by 46 publications

(26 citation statements)

References 29 publications

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“…The allele number per locus is the highest among the rice collections that have been reported to date [37], [40], including an Indian germplasm collection [41], an Indonesian landrace collection [42] and a Brazilian rice core collection [43], with an exception of an Indonesian traditional and improved rice collection with 13 alleles per locus reported by Thomson et al [44]. The average polymorphic information content (PIC) value in this study was 0.71, which is also the highest among previous studies for rice populations [37], [40], [41], [42], [44], [45] with an exception of 0.75 PIC value in a study reported by Borba et al [43]. The wide range of genetic diversity along with the manageable number of accessions in the URMC makes it one of the best collections for mining valuable genes in rice.…”

Section: Discussionmentioning

confidence: 99%

Unraveling the Complex Trait of Harvest Index with Association Mapping in Rice (Oryza sativa L.)

Wang

Agrama³

et al. 2012

PLoS ONE

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Harvest index is a measure of success in partitioning assimilated photosynthate. An improvement of harvest index means an increase in the economic portion of the plant. Our objective was to identify genetic markers associated with harvest index traits using 203 O. sativa accessions. The phenotyping for 14 traits was conducted in both temperate (Arkansas) and subtropical (Texas) climates and the genotyping used 154 SSRs and an indel marker. Heading, plant height and weight, and panicle length had negative correlations, while seed set and grain weight/panicle had positive correlations with harvest index across both locations. Subsequent genetic diversity and population structure analyses identified five groups in this collection, which corresponded to their geographic origins. Model comparisons revealed that different dimensions of principal components analysis (PCA) affected harvest index traits for mapping accuracy, and kinship did not help. In total, 36 markers in Arkansas and 28 markers in Texas were identified to be significantly associated with harvest index traits. Seven and two markers were consistently associated with two or more harvest index correlated traits in Arkansas and Texas, respectively. Additionally, four markers were constitutively identified at both locations, while 32 and 24 markers were identified specifically in Arkansas and Texas, respectively. Allelic analysis of four constitutive markers demonstrated that allele 253 bp of RM431 had significantly greater effect on decreasing plant height, and 390 bp of RM24011 had the greatest effect on decreasing panicle length across both locations. Many of these identified markers are located either nearby or flanking the regions where the QTLs for harvest index have been reported. Thus, the results from this association mapping study complement and enrich the information from linkage-based QTL studies and will be the basis for improving harvest index directly and indirectly in rice.

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Section: Discussionmentioning

confidence: 99%

Unraveling the Complex Trait of Harvest Index with Association Mapping in Rice (Oryza sativa L.)

Wang

Agrama³

et al. 2012

PLoS ONE

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“…M olecular marker are a powerful tool for the characterization and evaluation of genetic diversity, population structure, and relationship in plant germplasm collections and have been applied to cultivated rice ( Oryza sativa L.) (Garris et al, 2005; Alvarez et al, 2007; Zeng et al, 2007; Thomson et al, 2007, 2009; Jayamani et al, 2007; Agrama et al, 2007; Agrama and Eizenga, 2008), weedy rice ( Oryza sativa L.) (Gealy et al, 2009; Cao et al, 2006), bread wheat ( Triticum aestivum L.) and wild emmer wheat [ Triticum turgidum L. subsp. dicoccoides (Körn.…”

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confidence: 99%

“…Rice is one of the most important food crops because it feeds more than half of the world's population (Khush, 1997). Molecular markers have been used to study genetic diversity and interrelationships for rice cultivars in the United States (Mackill, 1995; Xu et al, 2004; Garris et al, 2005; Caicedo et al, 2007), China (Zeng et al, 2007; Zhang et al, 2009), Indonesia (Thomson et al, 2007, 2009), Portugal (Jayamani et al, 2007), and Cuba (Alvarez et al, 2007). These studies focused on different areas: either a group of cultivars of specific interest, or germplasm accessions from a certain region, or a portion of a germplasm collection.…”

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confidence: 99%

Geographic Description of Genetic Diversity and Relationships in the USDA Rice World Collection

Wang

Agrama²,

Jia

et al. 2010

Crop Science

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Knowledge of genetic diversity and relationships among global germplasms of rice collected by the USDA since 1866 is critical for utilization, conservation, and management of the collection. A core subset developed from this collection, including 1794 accessions obtained from 112 countries in 14 geographic regions, was genotyped with one indel and 71 simple sequence repeat (SSR) markers. Total alleles were 1005, averaging 14 alleles per locus. A great majority of genetic variance was due to within instead of among geographic regions and within instead of among countries. The regions and countries were highly and significantly differentiated using these markers. Germplasm accessions obtained from the southern Asia, Southeast Asia, and Africa were highly diversified, while those from North America and western and eastern Europe had the lowest diversity. Different measurements of genetic diversity, including average number of alleles per locus, polymorphism information content (PIC), Nei index, and average number of private alleles per locus uniformly reached this conclusion. Three main clusters were revealed by both analyses of principal coordinates and Nei genetic similarities for the 14 regions. Seventy‐eight countries, from which five or more accessions were collected in the core subset, were differentiated into five main clusters. Germplasm accessions obtained from Myanmar, Indonesia, Cambodia, Malaysia, and Nepal were highly diversified, while those from France, Spain, Romania, Italy, and the United States were poorly diversified. This study proves that the USDA global collection effectively supports the U.S. rice industry with vast genetic diversity responsive to biotic and abiotic stresses.

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“…This study directed to investigate and determine the genetic diversity and relationship of the tidal swamp rice germplasm of the South Kalimantan Province, Indonesia using the chloroplast trnL-F and nuclear IGS sequences. In a local scale, such studies could reveal the complex interaction between germplasm and farmers cultivation practices in good view [25]. Hence, the results of this study expected to be used as a reference in the rice genetic improvement and conservation program in the future.…”

Section: Introductionmentioning

confidence: 88%

Molecular Diversity of The Tidal Swamp Rice (<em>Oryza sativa</em> L.) Germplasm of The South Kalimantan, Indonesia

Mursyidin¹,

Purnomo²,

Sumardi³

et al. 2018

Preprint

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Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of sixteen cultivars of this germplasm, consisting of fifteen of the South Kalimantan Province and one of Sumatera Island, Indonesia (an outgroup) were analyzed, phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). The results showed that this germplasm has a relatively more extraordinary genetic diversity than other local rice germplasm. In a nucleotide level, this germplasm showed a genetic diversity of 0.61 for nuclear IGS and 0.58 for trnL-F. The phylogenetic reconstruction also exhibited that this germplasm has the unique illustration of phylogenetic trees, particularly for the combined sequence datasets. Thus, the results of our study would provide useful information for further understanding of evolutionary relationships of this germplasm and facilitate the efficient utilization of valuable genes for genetic improvement, particularly in the tidal swamp areas.

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Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo

Cited by 46 publications

References 29 publications

Unraveling the Complex Trait of Harvest Index with Association Mapping in Rice (Oryza sativa L.)

Unraveling the Complex Trait of Harvest Index with Association Mapping in Rice (Oryza sativa L.)

Geographic Description of Genetic Diversity and Relationships in the USDA Rice World Collection

Molecular Diversity of The Tidal Swamp Rice (<em>Oryza sativa</em> L.) Germplasm of The South Kalimantan, Indonesia

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