bims-plasge 2019-02-17 papers

Theor Appl Genet. 2019 Feb 14.

Development and validation of an exome-based SNP marker set for identification of the St, Jr and Jvs genomes of Thinopyrym intermedium in a wheat background.

Andras Cseh, Caiyun Yang, Stella Hubbart-Edwards, Duncan Scholefield, Stephen S Ashling, Amanda J Burridge, Paul A Wilkinson, Ian P King, Julie King, Surbhi Grewal.

KEY MESSAGE: Cytogenetic analysis and array-based SNP genotyping of wheat- Th. intermedium introgression lines allowed identification of 634 chromosome-specific SNP markers across all twenty-one chromosomes of Th. intermedium (StJ r J vs , 2 n = 6 x = 42). Thinopyrum intermedium (2n = 6x = 42, StJrJvs) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic diversity from wild species to wheat offers valuable responses to the effects of climate change. The new array-based single-nucleotide polymorphism (SNP) marker technology provides cheap and easy-to-use molecular markers for marker-assisted selection (MAS) in wheat breeding programmes. Here, we focus on the generation of a new chromosome-specific SNP marker set that can be used to characterize and identify the Th. intermedium chromosomes or chromosome segments transferred into wheat. A progressive investigation of marker development was conducted using 187 various newly developed wheat-Th. intermedium introgression lines and the Axiom® Wheat-Relative Genotyping array. We employed molecular cytogenetic techniques to clarify the genome constitution of the Th. intermedium parental lines and validated 634 chromosome-specific SNPs. Our data confirmed the allohexaploid nature of Th. intermedium and demonstrated that the St genome-specific GISH signal and markers are present at the centromeric regions of chromosomes 1Jvs, 2Jvs, 3Jvs and 7Jvs. The SNP markers presented here will be introduced into current wheat improvement programmes, offering a significant speed-up in wheat breeding and making it possible to deal with the transfer of the full genetic potential of Th. intermedium into wheat.

DOI: https://doi.org/10.1007/s00122-019-03300-9

Mol Genet Genomics. 2019 Feb 09.

Construction of genetic linkage map and genome dissection of domestication-related traits of moth bean (Vigna aconitifolia), a legume crop of arid areas.

Chutintorn Yundaeng, Prakit Somta, Kitiya Amkul, Alisa Kongjaimun, Akito Kaga, Norihiko Tomooka.

The moth bean (Vigna aconitifolia), possibly the most primitive crop of the genus Vigna, is a highly drought- and heat-resistant legume grown in arid areas. Moth bean domestication involved phenotypic changes, including reduction of seed dormancy and pod shattering, increased organ size, and earlier flowering and maturity. However, the genetics of the domestication process in moth bean is not known. In this study, we constructed a genetic linkage map for moth bean and used the map to identify quantitative trait loci (QTL) for domestication-related traits of an F2 population of 188 individuals produced from a cross of wild moth bean (TN67) and cultivated moth bean (ICPMO056). The genetic linkage map comprised 11 linkage groups (LG) of 172 simple sequence repeat markers and spanned a total length of 1016.8 centiMorgan (cM), with an average marker distance of 7.34 cM. A comparative genome analysis showed high genome synteny between moth bean and mungbean (Vigna radiata), adzuki bean (Vigna angularis), rice bean (Vigna umbellata), and yardlong bean (Vigna unguiculata). In total, 50 QTLs and 3 genes associated with 20 domestication-related traits were identified. Most of the QTLs belonged to five LGs (1, 2, 4, 7, and 10). Key traits related to domestication such as seed dormancy and pod shattering were controlled by large-effect QTLs (PVE > 20%) with one or two minor QTLs, whereas all other traits were controlled by one-seven minor QTLs, apart from seed weight, which was controlled by one major and seven minor QTLs. These results suggest that a small number of mutations with large phenotypic effects have contributed to the domestication of the moth bean. Comparative analysis of QTLs with related Vigna crops revealed that there are several domestication-related large-effect QTLs that had not been used in moth bean domestication. This study provides a basic genetic map and identified genome regions associated with domestication-related traits, which will be useful for the genetic improvement of the moth bean and related Vigna species.

Keywords: Domestication syndrome; Moth bean; Pod shattering; Seed dormancy; Vigna aconitifolia

DOI: https://doi.org/10.1007/s00438-019-01536-0

BMC Plant Biol. 2019 Feb 11. 19(1): 65

A quantitative proteomic analysis of the molecular mechanism underlying fertility conversion in thermo-sensitive genetic male sterility line AnnongS-1.

Siyao Wang, Qingyuan Tian, Shiqi Zhou, Dandan Mao, Liangbi Chen.

BACKGROUND: Thermo-sensitive genetic male sterile (TGMS) lines have been widely used in two-line hybrid rice breeding. The two-line hybrids have increased rice yields substantially. However, the effect of environmental temperatures on the fertility conversion is still not fully clear. In this study, we performed a tandem mass tag (TMT)-based proteomic analysis on the anthers of the TGMS line AnnongS-1 grown under permissive (low) temperature (21 °C) and restrictive (high) temperature (> 26 °C) conditions in an attempt to explore the effect of temperature on the fertility of the male sterile line.RESULTS: After the AnnongS-1 plants were induced under either permissive or restrictive conditions, morphological observations and I2-KI staining confirmed that the pollen grains formed under high temperature conditions were abortive while those formed under low temperature developed normally. In comparison to the plants grown under permissive conditions, the restrictive high-temperature conditions led to the differential accumulation of 89 proteins in the anthers, of which 46 were increased in abundance and 43 were decreased in abundance. Most of the subcellular compartments of the anther cells had one or more proteins that had been differentially accumulated, with the cytoplasm and chloroplast having the greatest accumulations. More than 40% of the differentially abundant proteins (DAPs) were enzymes involved in photosynthesis, energy metabolism, biosynthesis and catabolism of cellular components, metabolic regulation, defense and stress, etc. The DAPs related to protein metabolism accounted for the largest proportion (21.35%), followed by those related to defense and stress (12.36%), metabolic regulation (10.11%) and carbohydrate metabolism (8.99%), indicating that such biological processes in anther cells were more susceptible to high temperature stress.
CONCLUSIONS: The restrictive temperature induction caused fertility-sterility conversion in the TGMS line AnnongS-1 mainly by adversely affecting the metabolism of protein, carbohydrate and energy, and decreasing the abundances of important proteins closely related to defense and stress, thereby impeding the growth and development of the pollen and weakening the overall defense and ability to endure stress of AnnongS-1. These data are helpful for deepening our understanding of the molecular mechanism underlying fertility conversion in TGMS lines.

Keywords: AnnongS-1; Fertility conversion; Hybrid rice; Proteomics; Thermo-sensitive genetic male-sterility

DOI: https://doi.org/10.1186/s12870-019-1666-5

BMC Genomics. 2019 Feb 13. 20(1): 132

The plastid and mitochondrial genomes of Eucalyptus grandis.

Desre Pinard, Alexander A Myburg, Eshchar Mizrachi.

BACKGROUND: Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes.RESULTS: In order to facilitate further studies of cytonuclear interactions in Eucalyptus, we report an updated annotation of the E. grandis plastid genome, and the second sequenced and annotated mitochondrial genome of the Myrtales, that of E. grandis. The 478,813 bp mitochondrial genome shows the conserved protein coding regions and gene order rearrangements typical of land plants. There have been widespread insertions of organellar DNA into the E. grandis nuclear genome, which span 141 annotated nuclear genes. Further, we identify predicted editing sites to allow for the discrimination of RNA-sequencing reads between nuclear and organellar gene copies, finding that nuclear copies of organellar genes are not expressed in E. grandis.
CONCLUSIONS: The implications of organellar DNA transfer to the nucleus are often ignored, despite the insight they can give into the ongoing evolution of plant genomes, and the problems they can cause in many applications of genomics. Future comparisons of the transcription and regulation of organellar genes between Eucalyptus genotypes may provide insight to the cytonuclear interactions that impact economically important traits in this widely grown lignocellulosic crop species.

Keywords: Chloroplast; Eucalyptus grandis; Mitochondria; Organelle genome; Plastid

DOI: https://doi.org/10.1186/s12864-019-5444-4

Sci Rep. 2019 Feb 14. 9(1): 2060

Genome defense against integrated organellar DNA fragments from plastids into plant nuclear genomes through DNA methylation.

Takanori Yoshida, Hazuka Y Furihata, Taiko Kim To, Tetsuji Kakutani, Akira Kawabe.

Nuclear genomes are always faced with the modification of themselves by insertions and integrations of foreign DNAs and intrinsic parasites such as transposable elements. There is also substantial number of integrations from symbiotic organellar genomes to their host nuclear genomes. Such integration might have acted as a beneficial mutation during the evolution of symbiosis, while most of them have more or less deleterious effects on the stability of current genomes. Here we report the pattern of DNA substitution and methylation on organellar DNA fragments integrated from plastid into plant nuclear genomes. The genome analyses of 17 plants show homology-dependent DNA substitution bias. A certain number of these sequences are DNA methylated in the nuclear genome. The intensity of DNA methylation also decays according to the increase of relative evolutionary times after being integrated into nuclear genomes. The methylome data of epigenetic mutants shows that the DNA methylation of organellar DNA fragments in nuclear genomes are mainly dependent on the methylation maintenance machinery, while other mechanisms may also affect on the DNA methylation level. The DNA methylation on organellar DNA fragments may contribute to maintaining the genome stability and evolutionary dynamics of symbiotic organellar and their host's genomes.

DOI: https://doi.org/10.1038/s41598-019-38607-6