Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

Background: Availability of related rice species is critical for rice breeding and improvement. Two distinct species of domesticated rice exist in the genus Oryza: Oryza sativa (Asian rice) and Oryza glaberrima (African rice). New rice for Africa (NERICA) is derived from interspecific crosses between these two species. Molecular profiling of these germplasms is important for both genetics and breeding studies. We used 30 polymorphic SSR markers to assess the genetic diversity and molecular fingerprints of 53 rice genotypes of O. sativa, O. glaberrima, and NERICA. Results: In total, 180 alleles were detected. Average polymorphism information content and Shannon's information index were 0.638 and 1.390, respectively. Population structure and neighbor-joining phylogenetic tree revealed that 53 genotypes grouped into three distinct subpopulations conforming to the original three groups, except three varieties (IR66417, WAB450-4, MZCD74), and that NERICA showed a smaller genetic distance from O. sativa genotypes (0.774) than from O. glaberrima genotypes (0.889). A molecular fingerprint map of the 53 accessions was constructed with a novel encoding method based on the SSR polymorphic alleles. Ten specific SSR markers displayed different allelic profiles between the O. glaberrima and O. sativa genotypes. Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms

Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

Background: Availability of related rice species is critical for rice breeding and improvement. Two distinct species of domesticated rice exist in the genus Oryza: Oryza sativa (Asian rice) and Oryza glaberrima (African rice). New rice for Africa (NERICA) is derived from interspecific crosses between these two species. Molecular profiling of these germplasms is important for both genetics and breeding studies. We used 30 polymorphic SSR markers to assess the genetic diversity and molecular fingerprints of 53 rice genotypes of O. sativa, O. glaberrima, and NERICA. Results: In total, 180 alleles were detected. Average polymorphism information content and Shannon's information index were 0.638 and 1.390, respectively. Population structure and neighbor-joining phylogenetic tree revealed that 53 genotypes grouped into three distinct subpopulations conforming to the original three groups, except three varieties (IR66417, WAB450-4, MZCD74), and that NERICA showed a smaller genetic distance from O. sativa genotypes (0.774) than from O. glaberrima genotypes (0.889). A molecular fingerprint map of the 53 accessions was constructed with a novel encoding method based on the SSR polymorphic alleles. Ten specific SSR markers displayed different allelic profiles between the O. glaberrima and O. sativa genotypes. Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms. Keywords: African rice, Asian rice, Fingerprinting, Food security, Genetic relationship, Microsatellite markers, Molecular profiling, Phylogenetic tree, Polymorphic alleles, Rice breeding, SS

The Asian lotus (Nelumbo nucifera) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics

The Asian lotus (Nelumbo nucifera) has a history of cultivation in Asia dating back over 3,000 years where it has been an important food crop producing edible rhizomes and seeds as well as flowers of great aesthetic and cultural value. Here, we de novo assembled the plastomes of 316 lotus accessions including five North American lotus (N. lutea) and 311 Asian lotus (N. nucifera) to construct a pan-plastome genome map, and investigate the phylogeography and genetic diversity among the only two extant species within this living fossil lineage. A total of 113 unique genes were annotated and plastome sizes varied between 163,457 and 163,672 bp with only minor differences in each of the four major genomic units. The most abundant nucleotide differences among plastomes were single nucleotide variants followed by insertions/deletions and block substitutions mainly found in intergenic spacer regions of the large single copy portion of the plastome. Seven well-supported genetic clusters were resolved using multiple different population structure analyses. The different lotus types (flower, seed, rhizome, or wild) were disproportionally assigned to multiple different genetic clusters. This pattern indicates that the domestication of Asian lotus involved multiple genetic origins and possible matrilineal introgression. Geographic mapping of accessions also revealed that genetic diversity is unevenly distributed with eastern China possessing the highest genetic diversity and regions such as Yunnan, Indonesian, and Thailand possessing unique haplotypes. These results provide an important maternal history of Nelumbo and necessary groundwork for future studies on intergenomic gene transfer, cytonuclear incompatibility, and conservation genetics

Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences

Lagerstroemia L. (Lythraceae) is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia, with numerous species highly valued as ornamentals. Although the plastomes of many species in this genus have been sequenced, the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined. We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses. Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods. Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility. These results as well as analyses of non-synonymous and synonymous mutations, indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution. In addition, divergence events within the Lagerstroemia were dated for the first time. Several of the divergence estimates corresponded to well-known Earth history events, such as the reduction in global temperatures at the Eocene/Oligocene boundary. Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders, as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species

Population Genetic Analysis of a Bread Wheat Panel from Northern and Huang-Huai Agro-Ecological Regions in China

Bread wheat (Triticum aestivum L.) is one of the most extensively cultivated cereal crops around the world. Here, we investigated the population structure and genetic diversity of a panel mainly originated from two wheat agro-ecological regions (northern winter wheat region, NW; and the Huang-Huai River Valley’s facultative wheat region, HH) in China based on a 15K SNP array. Population genetic analysis revealed that the optimal population number (K) was three, and the three groups were roughly related to ecological regions, including NW (mainly Hebei), HH1 (Henan-Shaanxi), and HH2 (Shandong). Within HH, HH1 had a higher nucleotide diversity (π = 0.31167), minor allele frequency (MAF = 0.2663), polymorphism information content (PIC = 0.2668), and expected heterozygosity (Hexp = 0.3346) than HH2. Furthermore, our results demonstrated that genetic diversity decreases with the advancement of wheat breeding. Finally, inference of ancestry informative markers indicated that the genomes of the three pure groups from the three provinces (Hebei, Henan, and Shandong) of the two regions have genomic regions with different mosaic patterns derived from the two landrace groups. These findings may facilitate the development of wheat breeding strategies to target novel desired alleles in the future

Genetic Diversity and Phenotypic Variation in an Introgression Line Population Derived from an Interspecific Cross between <i>Oryza glaberrima</i> and <i>Oryza sativa</i>

<div><p>The introduction of closely related species genomic fragments is an effective way to enrich genetic diversity and creates new germplasms in crops. Here, we studied the genetic diversity of an introgression line (IL) population composed of 106 ILs derived from an interspecific tetra cross between <i>O</i>. <i>glaberrima</i> and <i>O</i>. <i>sativa</i> (RAM3/Jin23B//Jin23B///YuetaiB). The proportion of <i>O</i>. <i>glaberrima</i> genome (PGG) in the ILs ranged from 0.3% to 36.7%, with an average value of 12.32% which is close to the theoretically expected proportion. A total of 250 polymorphic alleles were amplified by 21 AFLP primer combinations with an average of 12 alleles per primer. Population structure analysis revealed that the IL population can be divided into four genetically distinct subpopulations. Both principal component analysis and neighbor-joining tree analysis showed that ILs with a higher PGG displayed greater genetic diversity. Canonical discriminant analysis identified six phenotypic traits (plant height, yield per plant, filled grain percentage, panicle length, panicle number and days to flowering) as the main discriminatory traits among the ILs and between the subpopulations and showed significant phenotypic distances between subpopulations. The effects of PGG on phenotypic traits in the ILs were estimated using a linear admixed model, which showed a significant positive effect on grain yield per plant (0.286±0.117), plant height (0.418 ± 0.132), panicle length (0.663 ± 0.107), and spikelet number per panicle (0.339 ± 0.128), and a significant negative effect on filled grain percentage (-0.267 ± 0.123) and days to flowering (-0.324 ± 0.075). We found that an intermediate range (10% − 20%) of PGG was more effective for producing ILs with favorable integrated agronomic traits. Our results confirm that construction of IL population carrying <i>O</i>. <i>glaberrima</i> genomic fragments could be an effective approach to increase the genetic diversity of <i>O</i>. <i>sativa</i> genome and an appropriate level of PGG could facilitate pyramiding more favorable genes for developing more adaptive and productive rice.</p></div

Phenotypic traits in ILs with different PGGs.

<p>1: PGG < 10%, 2: 10% ≤ PGG < 20%, 3: 20% ≤ PGG < 30%, 4: 30% ≤ PGG < 40%.</p

Pairwise Pearson’s correlations between PGG or FVL and phenotypic traits in ILs.

<p>Pairwise Pearson’s correlations between PGG or FVL and phenotypic traits in ILs.</p

Comparison of two matrixes of pairwise DIST distances between ILs based on AFLP markers and phenotypic traits.

<p>Lower left (a): Matrix of pairwise DIST distances between ILs based on AFLP markers; (b): The structure of the IL population; Upper right (c): The PGG in ILs; (d): Matrix of pairwise DIST distances between ILs based on phenotypic traits.</p