Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

Duan, Shi-Hua; Lu, Bao‐Rong; Li, Zhong; Tong, Jiping; Kong, Jin; Yi, Wen; Li, Shaoqing; Zhu, Yong‐Guan

doi:10.1007/s10528-006-9062-x

Cited by 38 publications

(40 citation statements)

References 54 publications

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“…Some genes such as Rhz2, Rhz3, and Xa21 have been identified and have been used for developing perennial rice (Hu et al 2003 and blight disease resistance (Song et al 1995), but so far O. longistaminata has been little utilized for rice improvement. It is considerably diverged from O. sativa as compared to the other AA species (Ren et al 2003, Duan et al 2007, and is reproductively isolated from the others by hybrid sterility and embryo abortion (Causse et al 1994. To obtain F 1 inter-specific progeny, embryo rescue is usually required, and hybrid sterility is a common phenomenon in backcross generations.…”

Section: Introductionmentioning

confidence: 99%

QTL analysis for hybrid sterility and plant height in interspecific populations derived from a wild rice relative, Oryza longistaminata

Chen

et al. 2009

Breed. Sci.

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Hybrid sterility is a serious barrier in the utilization of wild rice for breeding, but little is known regarding hybrid sterility between the cultivated rice, Oryza sativa, and its wild relative, O. longistaminata. In order to understand further the nature of interspecific hybrid sterility, pollen and spikelet fertility were investigated in two BC 7 F 2 populations derived from a semisterile individual of BC 5 F 1 between Oryza sativa L. and O. longistaminata. One main-effect QTL for pollen and spikelet fertility qpsf6 was detected on the short arm of chromosome 6 close to RM587, around it favoring O. longistaminata allele was found. Comparing the position and effect with other studies indicated that this QTL coincides with the gamete eliminator, S1. It suggests that there exists an orthologous hybrid sterility locus that controls the reproduction barrier between O. sativa and its AA genome relatives. QTL mapping for plant height was also conducted in one of the BC 7 F 2 populations. One QTL, qph1, was detected on the long arm of chromosomes 1 close to RM6333 and coincides with the semi-dwarf gene, sd-1. These new QTL information will increase the efficiency of cultivar development via interspecific hybridization involving O. longistaminata, and offset the stage for fine mapping of these QTL.

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Section: Introductionmentioning

confidence: 99%

QTL analysis for hybrid sterility and plant height in interspecific populations derived from a wild rice relative, Oryza longistaminata

Chen

et al. 2009

Breed. Sci.

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“…The randomly amplified polymorphic DNA (RAPD) technique (Williams et al 1990) has been extensively used in the study of genetic markers and genetic divergence and in the system classification of animals, plants, and microorganisms (Yan et al 2007;Geng et al 2007;Duan et al 2007;Chen et al 2005;Chang et al 2003). Genetic markers are important in the investigation of the phylogeny of animals and plants (Li et al 2000;Meng et al 1996) as well as the relationships between their genetic structure and useful properties (Moriuchi and Winn 2005;Cheres et al 2000;Machon et al 2003).…”

Section: Introductionmentioning

confidence: 99%

Relationships Among Genetic Makeup, Active Ingredient Content, and Place of Origin of the Medicinal Plant Gastrodia Tuber

et al. 2008

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Gastrodia tuber and its component gastrodin have many pharmacological effects. The chemical fingerprints and gastrodin contents of eight Gastrodia populations were determined, and the genomic DNA polymorphism of the populations was investigated. Genetic distance coefficients among the populations were calculated using the DNA polymorphism data. A dendrogram of the genetic similarities between the populations was constructed using the genetic distance coefficients. The results indicated that the genomic DNA of Gastrodia tubers was highly polymorphic; the eight populations clustered into three major groups, and the gastrodin content varied greatly among these groups. There were obvious correlations among genetic makeup, gastrodin content, and place of origin. The ecological environments in Guizhou and Shanxi may be conducive to evolution and to gastrodin biosynthesis, and more suitable for cultivation of Gastrodia tubers. These findings may provide a scientific basis for overall genetic resource management and for the selection of locations for cultivating Gastrodia tubers.

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“…The tree is not drawn to scale. American origin (Givnish et al 2004;Groeneveld et al 2007 Duan et al (2007) and Kumagai et al (2010) in phylogenetic studies conducted using mitochondria and chloroplast DNA sequences respectively, where the two species formed monophyletic clades. In addition to phylogenetic analysis, the use of molecular clock is commonly used to gain insights on the origin and evolution of species.…”

Section: Molecular Divergence Datingmentioning

confidence: 99%

Genomic characterization of African cultivated and wild Oryza species

Wambugu¹

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Rice is the most important crop in the world, acting as the staple food for over half of the world's population. It belongs to the Oryza genus and has a wide genetic diversity of both wild and cultivated species, with a substantial proportion of this diversity being found in Africa. In this thesis, African cultivated and wild Oryza species have been characterized using genomic tools with the goal of promoting their conservation and utilization. A desk based study aimed at documenting the current state of conservation and utilization of African Oryza genetic resources revealed that they remain under collected and hence underrepresented in germplasm collections. Moreover, they are under-characterized and therefore grossly underutilized. In order to obtain maximum benefits from these resources, it is imperative that they are collected, efficiently conserved and optimally utilized. Efficient conservation and utilization of the Oryza gene pool is however hindered by lack of conclusive, consistent and well resolved phylogenetic and evolutionary relationships between the various cultivated and wild species. This study therefore sought to define the genetic and evolutionary relationships between the various wild and cultivated African species that form part of the AA genome group. This was done by reconstructing the phylogeny of Oryza AA genome species by massive parallel sequencing of whole chloroplast genomes. The analysis resulted in a well resolved and strongly supported phylogeny of the AA genome species showing strong genetic differentiation.The clearly defined relationships between the various taxa provide a robust platform for supporting the conservation and utility of these species. In an effort at promoting utility of these species, their starch physicochemical properties and the functional diversity relating to these starch related traits were analyzed. African rice was found to have some unique starch structure and properties, among these being high amylose content which is higher than in Asian rice. Amylose content is a key starch trait in rice. The health benefits of high amylose foods are increasingly getting recognized. African rice therefore seems to be a valuable genetic resource for breeding premium-value genotypes with high amylose content. The deployment of African rice genetic resources in rice improvement is however constrained by the inadequate understanding of the genetic mechanism underlying their unique starch traits, specifically amylose content. First, this study analysed key starch biosynthesis genes in the genomes of various cultivated and wild Oryza species. The analysis revealed that the pullulanase gene has undergone gene duplication in African rice. This apparent gene duplication was characterized with the aim of understanding whether itiii could be the molecular mechanism underlying high amylose in African rice. It was hypothesized that this gene duplication may have led to increased pullulanase activity which may have subsequently led to unique starch structure and properties...

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Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

Cited by 38 publications

References 54 publications

QTL analysis for hybrid sterility and plant height in interspecific populations derived from a wild rice relative, Oryza longistaminata

QTL analysis for hybrid sterility and plant height in interspecific populations derived from a wild rice relative, Oryza longistaminata

Relationships Among Genetic Makeup, Active Ingredient Content, and Place of Origin of the Medicinal Plant Gastrodia Tuber

Genomic characterization of African cultivated and wild Oryza species

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