bims-plasge 2021-08-01 papers

Issue of 2021–08–01
four papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Plant J. 2021 Jul 26.

Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number.

Matheus Fernandes Gyorfy, Emma R Miller, Justin L Conover, Corrinne E Grover, Jonathan F Wendel, Daniel B Sloan, Joel Sharbrough.

The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication events (WGDs) in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follow WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR (ddPCR) to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.

Keywords: Aegilops speltoides ; Arabidopsis arenosa ; Arabidopsis suecica ; Arabidopsis thaliana ; Triticum aestivum ; Triticum turgidum ; Triticum urartu ; Chloroplast; Cytonuclear Interactions; Mitochondria; Polyploidy; Whole Genome Duplications

DOI: https://doi.org/10.1111/tpj.15436

Plant Sci. 2021 Sep;pii: S0168-9452(21)00153-9. [Epub ahead of print]310 110957

Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum.

Timo Hellwig, Shahal Abbo, Amir Sherman, Ron Ophir.

Plant breeders and conservationist depend on knowledge about the genetic variation of their species of interest. Pisum fulvum, a wild relative of domesticated pea, has attracted attention as a genetic resource for crop improvement, yet little information about its diversity in the wild has been published hitherto. We sampled 15 populations of P. fulvum from Israeli natural habitats and conducted genotyping by sequencing to analyse their genetic diversity and adaptive state. We also attempted to evaluate the species past demography and the prospects of its future reaction to environmental changes. The results suggest that genetic diversity of P. fulvum is low to medium and is distributed between well diverged populations. Surprisingly, with 56 % in the total population the selfing rate was found to be significantly lower than expected from a species that is commonly assumed to be a predominant selfer. We found a strong genetic bottleneck during the last glacial period and only limited patterns of isolation by distance and environment, which explained 13 %-18 % of the genetic variation. Despite the weak signatures of genome-wide IBE, 1,354 markers were significantly correlated with environmental factors, 1,233 of which were located within known genes with a nonsynonymous to synonymous ratio of 0.382. Species distribution modelling depicted an ongoing fragmentation and decreased habitable area over the next 80 years under two different socio-economic pathways. Our results suggest that complex interactions of substantial drift and selection shaped the genome of P. fulvum. Climate changeis likely to cause further erosion of genetic diversity in P. fulvum. Systematic ex-situ conservation may be advisable to safeguard genetic variability for future utilization of this species.

Keywords: Adaptation; Climate change; Crop wild relative; Diversity; Pisum

DOI: https://doi.org/10.1016/j.plantsci.2021.110957

Theor Appl Genet. 2021 Jul 30.

Dissecting the genetic control of seed coat color in a RIL population of common bean (Phaseolus vulgaris L.).

Carmen García-Fernández, Ana Campa, Juan Jose Ferreira.

KEY MESSAGE: Three genes associated with the seed coat color in a TU/Musica RIL population were located on a genetic map, and two candidate genes proposed to control black seed coat in the TU genotype were characterized. Seed coat color is an important characteristic of common bean (Phaseolus vulgaris L.) associated with the marketability of dry bean cultivars, quality and nutritional characteristics of seed, as well as response to pathogens. In this study, the genetic control of seed coat color in a recombinant inbred line population (175 lines) obtained from the cross 'TU' × 'Musica' was investigated. Phenotypic segregation fitted 1:1 for white vs. nonwhite, and 3:1 for brown versus black, indicating the involvement of three independent genes, one controlling white color and two (with epistatic interaction) controlling black color. Using a genetic map built with 842 SNPs, the gene responsible for the white seed coat was mapped on the linkage group Pv07, in the position previously described for the P gene. For the black seed coat phenotype, two genes were mapped to the beginning of chromosomes Pv06 and Pv08, in the positions estimated for the V gene and the complex C locus, respectively, by classical studies. The involvement of these two genomic regions was verified through two crosses between three selected RILs exhibiting complementary and dominant inheritance, in which the TU alleles for both genes resulted in a black phenotype. Two genes involved in the anthocyanin biosynthesis pathway were proposed as candidate genes: Phvul.006G018800 encoding a flavonoid 3'5'hydroxylase and Phvul.008G038400 encoding MYB113 transcription factor. These findings add knowledge to the complex network of genes controlling seed coat color in common bean as well as providing genetic markers to be used in future genetic analysis or plant breeding.

DOI: https://doi.org/10.1007/s00122-021-03922-y

J Genet Genomics. 2021 Jun 07. pii: S1673-8527(21)00139-9. [Epub ahead of print]

Sporophytic control of anther development and male fertility by glucose-6-phosphate/phosphate translocator 1 (OsGPT1) in rice.

Aili Qu, Yan Xu, Xinxing Yu, Qi Si, Xuwen Xu, Changhao Liu, Liuyi Yang, Yueping Zheng, Mengmeng Zhang, Shuqun Zhang, Juan Xu.

Coordination between the sporophytic tissue and the gametic pollen within anthers is tightly controlled to achieve the optimal pollen fitness. Glucose-6-phosphate/phosphate translocator (GPT) transports glucose-6-phosphate, a key precursor of starch and/or fatty acid biosynthesis, into plastids. Here, we report the functional characterization of OsGPT1 in the rice anther development and pollen fertility. Pollen grains from homozygous osgpt1 mutant plants fail to accumulate starch granules, resulting in pollen sterility. Genetic analyses reveal a sporophytic effect for this mutation. OsGPT1 is highly expressed in the tapetal layer of rice anther. Degeneration of the tapetum, an important process to provide cellular contents to support pollen development, is impeded in osgpt1 plants. In addition, defective intine and exine are observed in the pollen from osgpt1 plants. Expression levels of multiple genes that are important to tapetum degeneration or pollen wall formation are significantly decreased in osgpt1 anthers. Previously, we reported that AtGPT1 plays a gametic function in the accumulation of lipid bodies in Arabidopsis pollen. This report highlights a sporophytic role of OsGPT1 in the tapetum degeneration and pollen development. The divergent functions of OsGPT1 and AtGPT1 in pollen development might be a result of their independent evolution after monocots and dicots diverged.

Keywords: Glucose-6-phosphate/phosphate translocator; Intine and exine formation; Male fertility; Pollen development; Rice; Sporophytic control; Starch accumulation; Tapetum degeneration

DOI: https://doi.org/10.1016/j.jgg.2021.04.013