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9. Transcriptome Analysis of the Differentially Expressed Genes in the Male and Female Shrub Willows (Salix suchowensis).

Author

Liu, Jingjing, Yin, Tongming, Ye, Ning, Chen, Yingnan, Yin, Tingting, Liu, Min, and Hassani, Danial

Subjects
*TRANSCRIPTION factors, *GENE expression in plants, *SHRUBS, *DIOECIOUS plants, *WILLOWS, *ANGIOSPERMS, *PLANT evolution
Abstract

Background: The dioecious system is relatively rare in plants. Shrub willow is an annual flowering dioecious woody plant, and possesses many characteristics that lend it as a great model for tracking the missing pieces of sex determination evolution. To gain a global view of the genes differentially expressed in the male and female shrub willows and to develop a database for further studies, we performed a large-scale transcriptome sequencing of flower buds which were separately collected from two types of sexes. Results: Totally, 1,201,931 high quality reads were obtained, with an average length of 389 bp and a total length of 467.96 Mb. The ESTs were assembled into 29,048 contigs, and 132,709 singletons. These unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases and assigned with Gene Ontology (GO) terms. A biochemical pathway database containing 291 predicted pathways was also created based on the annotations of the unigenes. Digital expression analysis identified 806 differentially expressed genes between the male and female flower buds. And 33 of them located on the incipient sex chromosome of Salicaceae, among which, 12 genes might involve in plant sex determination empirically. These genes were worthy of special notification in future studies. Conclusions: In this study, a large number of EST sequences were generated from the flower buds of a male and a female shrub willow. We also reported the differentially expressed genes between the two sex-type flowers. This work provides valuable information and sequence resources for uncovering the sex determining genes and for future functional genomics analysis of Salicaceae spp. [ABSTRACT FROM AUTHOR]

Published
2013
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10. Transcriptome Analysis of the Differentially Expressed Genes in the Male and Female Shrub Willows (Salix suchowensis).

Author

Liu, Jingjing, Yin, Tongming, Ye, Ning, Chen, Yingnan, Yin, Tingting, Liu, Min, and Hassani, Danial

Subjects
TRANSCRIPTION factors, GENE expression in plants, SHRUBS, DIOECIOUS plants, WILLOWS, ANGIOSPERMS, PLANT evolution
Abstract

Background: The dioecious system is relatively rare in plants. Shrub willow is an annual flowering dioecious woody plant, and possesses many characteristics that lend it as a great model for tracking the missing pieces of sex determination evolution. To gain a global view of the genes differentially expressed in the male and female shrub willows and to develop a database for further studies, we performed a large-scale transcriptome sequencing of flower buds which were separately collected from two types of sexes. Results: Totally, 1,201,931 high quality reads were obtained, with an average length of 389 bp and a total length of 467.96 Mb. The ESTs were assembled into 29,048 contigs, and 132,709 singletons. These unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases and assigned with Gene Ontology (GO) terms. A biochemical pathway database containing 291 predicted pathways was also created based on the annotations of the unigenes. Digital expression analysis identified 806 differentially expressed genes between the male and female flower buds. And 33 of them located on the incipient sex chromosome of Salicaceae, among which, 12 genes might involve in plant sex determination empirically. These genes were worthy of special notification in future studies. Conclusions: In this study, a large number of EST sequences were generated from the flower buds of a male and a female shrub willow. We also reported the differentially expressed genes between the two sex-type flowers. This work provides valuable information and sequence resources for uncovering the sex determining genes and for future functional genomics analysis of Salicaceae spp. [ABSTRACT FROM AUTHOR]

Published
2013
Full Text
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11. Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits

Author

Alberto Palmonari, E. Charles Brummer, Paolo Annicchiarico, Elisa Biazzi, Luciano Pecetti, Aldo Tava, Nelson Nazzicari, and Yin, Tongming

Subjects
0106 biological sciences, 0301 basic medicine, Germplasm, Leaves, Surfactants, lcsh:Medicine, Plant Science, Lignin, Biochemistry, 01 natural sciences, Medicago, lcsh:Science, Flowering Plants, Genome, Multidisciplinary, Plant Biochemistry, Plant Anatomy, Chromosome Mapping, food and beverages, Fabaceae, Agriculture, Genomics, Single Nucleotide, Plants, Legumes, Chemistry, Neutral Detergent Fiber, Phenotype, Physical Sciences, Genome, Plant, Research Article, Medicago sativa, Biotechnology, Genetic Markers, General Science & Technology, Materials Science, Detergents, Quantitative Trait Loci, Forage, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Quantitative Trait, 03 medical and health sciences, Quantitative Trait, Heritable, Genomic Medicine, Genetic, Genome-Wide Association Studies, Genetics, Plant breeding, Selection, Genetic, Polymorphism, Heritable, Selection, Materials by Attribute, Selection (genetic algorithm), Alfalfa, Human Genome, fungi, lcsh:R, Organisms, Chemical Compounds, Biology and Life Sciences, Computational Biology, Human Genetics, Molecular Sequence Annotation, Plant, Genome Analysis, Agronomy, Plant Breeding, 030104 developmental biology, Genetic marker, lcsh:Q, Genome-Wide Association Study, 010606 plant biology & botany
Abstract

Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest). Trait-marker analyses were performed on progeny values averaged over conditions, owing to modest germplasm × condition interaction. Genomic selection exploited 11,450 polymorphic SNP markers, whereas a subset of 8,494 M. truncatula-aligned markers were used for a genome-wide association study (GWAS). GWAS confirmed the polygenic control of quality traits and, in agreement with phenotypic correlations, indicated substantially different genetic control of a given trait in stems and leaves. It detected several SNPs in different annotated genes that were highly linked to stem protein content. Also, it identified a small genomic region on chromosome 8 with high concentration of annotated genes associated with leaf ADL, including one gene probably involved in the lignin pathway. Three genomic selection models, i.e., Ridge-regression BLUP, Bayes B and Bayesian Lasso, displayed similar prediction accuracy, whereas SVR-lin was less accurate. Accuracy values were moderate (0.3-0.4) for stem NDFD and leaf protein content, modest for leaf ADL and NDFD, and low to very low for the other traits. Along with previous results for the same germplasm set, this study indicates that GBS data can be exploited to improve both quality traits (by genomic selection or MAS) and forage yield.

Published
2017

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