bims-plasge 2022-01-23 papers

Issue of 2022–01–23
six papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Genes (Basel). 2022 Jan 14. pii: 139. [Epub ahead of print]13(1):

OTP970 Is Required for RNA Editing of Chloroplast ndhB Transcripts in Arabidopsis thaliana.

Mei Fu, Xiaona Lin, Yining Zhou, Chunmei Zhang, Bing Liu, Dongru Feng, Jinfa Wang, Hongbin Wang, Honglei Jin.

RNA editing is essential for compensating for defects or mutations in haploid organelle genomes and is regulated by numerous trans-factors. Pentatricopeptide repeat (PPR) proteins are the prime factors that are involved in RNA editing; however, many have not yet been identified. Here, we screened the plastid-targeted PLS-DYW subfamily of PPR proteins belonging to Arabidopsis thaliana and identified ORGANELLE TRANSCRIPT PROCESSING 970 (OTP970) as a key player in RNA editing in plastids. A loss-of-function otp970 mutant was impaired in RNA editing of ndhB transcripts at site 149 (ndhB-C149). RNA-immunoprecipitation analysis indicated that OTP970 was associated with the ndhB-C149 site. The complementation of the otp970 mutant with OTP970 lacking the DYW domain (OTP970∆DYW) failed to restore the RNA editing of ndhB-C149. ndhB gene encodes the B subunit of the NADH dehydrogenase-like (NDH) complex; however, neither NDH activity and stability nor NDH-PSI supercomplex formation were affected in otp970 mutant compared to the wild type, indicating that alteration in amino acid sequence is not necessary for NdhB function. Together, these results suggest that OTP970 is involved in the RNA editing of ndhB-C149 and that the DYW domain is essential for its function.

Keywords: Arabidopsis; OTP970; PPR; RNA editing; chloroplast; ndhB-C149

DOI: https://doi.org/10.3390/genes13010139

Plant J. 2022 Jan 21.

Phylogeny and disparate selection signatures suggest two genetically independent domestication events of pea (Pisum L.).

Timo Hellwig, Shahal Abbo, Ron Ophir.

Domestication is considered as a model of adaptation which can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights on how plants react to different intensities of human manipulation, which has direct implication for the ongoing efforts of crop improvement. Therefore, scientists of various disciplines study domestication related questions to understand its biological and cultural bases. We employed RAD-sequencing of 494 pea samples from all wild and domesticated groups to analyse the collection's genetic structure. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect selection signatures putatively associated with domestication. Analysis of subpopulation structure of wild Pisum sativum exposed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex without indication for a hybrid origin. We detected 32 genomic regions putatively subjected to selection, 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild Pisum sativum is structured into well diverged subgroups. While P. s. ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplam. The two cultivated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.

Keywords: crop wild relative; domestication; genetic diversity; introgression; phylogeny; signatures of selection

DOI: https://doi.org/10.1111/tpj.15678

Genes (Basel). 2021 Dec 24. pii: 49. [Epub ahead of print]13(1):

Hormonal Influences on Pod-Seed Intercommunication during Pea Fruit Development.

Mark Bal, Lars Østergaard.

Angiosperms (from the Greek "angeion"-vessel, and "sperma"-seed) are defined by the presence of specialised tissue surrounding their developing seeds. This tissue is known as the ovary and once a flower has been fertilised, it gives rise to the fruit. Fruits serve various functions in relation to the seeds they contain: they often form tough physical barriers to prevent mechanical damage, they may form specialised structures that aid in dispersal, and they act as a site of nutrient and signal exchange between the parent plant and its offspring. The close coordination of fruit growth and seed development is essential to successful reproduction. Firstly, fertilisation of the ovules is required in most angiosperm species to initiate fruit growth. Secondly, it is crucial that seed dispersal facilitated by, e.g., fruit opening or ripening occurs only once the seeds have matured. These highly coordinated events suggest that seeds and fruits are in close communication throughout development and represent a classical problem of interorgan signalling and organismic resource allocation. Here, we review the contribution of studies on the edible, unicarpellate legume Pisum sativum to our understanding of seed and fruit growth coregulation, and propose areas of new research in this species which may yield important advances for both pulse agronomy and natural science.

Keywords: 4-chloroindole-3-acetic acid; auxin; development; pea; reproduction; signalling; starch; trehalose-6-phosphate

DOI: https://doi.org/10.3390/genes13010049

Hortic Res. 2022 Jan 19. pii: uhab062. [Epub ahead of print]

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history.

Stefano Pavan, Chiara Delvento, Nelson Nazzicari, Barbara Ferrari, Nunzio D'Agostino, Francesca Taranto, Concetta Lotti, Luigi Ricciardi, Paolo Annicchiarico.

Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections - a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.

DOI: https://doi.org/10.1093/hr/uhab062

Plant Mol Biol. 2022 Jan 17.

Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex.

Salah E Abdel-Ghany, Lisa M LaManna, Haleakala T Harroun, Pal Maliga, Daniel B Sloan.

KEY MESSAGE: Replacing the native clpP1 gene in the Nicotiana plastid genome with homologs from different donor species showed that the extent of genetic incompatibilities depended on the rate of sequence evolution. The plastid caseinolytic protease (Clp) complex plays essential roles in maintaining protein homeostasis and comprises both plastid-encoded and nuclear-encoded subunits. Despite the Clp complex being retained across green plants with highly conserved protein sequences in most species, examples of extremely accelerated amino acid substitution rates have been identified in numerous angiosperms. The causes of these accelerations have been the subject of extensive speculation but still remain unclear. To distinguish among prevailing hypotheses and begin to understand the functional consequences of rapid sequence divergence in Clp subunits, we used plastome transformation to replace the native clpP1 gene in tobacco (Nicotiana tabacum) with counterparts from another angiosperm genus (Silene) that exhibits a wide range in rates of Clp protein sequence evolution. We found that antibiotic-mediated selection could drive a transgenic clpP1 replacement from a slowly evolving donor species (S. latifolia) to homoplasmy but that clpP1 copies from Silene species with accelerated evolutionary rates remained heteroplasmic, meaning that they could not functionally replace the essential tobacco clpP1 gene. These results suggest that observed cases of rapid Clp sequence evolution are a source of epistatic incompatibilities that must be ameliorated by coevolutionary responses between plastid and nuclear subunits.

Keywords: Cytonuclear coevolution; Epistasis; Nicotiana; Plastome editing; Silene; clpP

DOI: https://doi.org/10.1007/s11103-022-01241-4

Front Plant Sci. 2021 ;12 718713

Pea Grain Protein Content Across Italian Environments: Genetic Relationship With Grain Yield, and Opportunities for Genome-Enabled Selection for Protein Yield.

Margherita Crosta, Nelson Nazzicari, Barbara Ferrari, Luciano Pecetti, Luigi Russi, Massimo Romani, Giovanni Cabassi, Daniele Cavalli, Adriano Marocco, Paolo Annicchiarico.

Wider pea (Pisum sativum L.) cultivation has great interest for European agriculture, owing to its favorable environmental impact and provision of high-protein feedstuff. This work aimed to investigate the extent of genotype × environment interaction (GEI), genetically based trade-offs and polygenic control for crude protein content and grain yield of pea targeted to Italian environments, and to assess the efficiency of genomic selection (GS) as an alternative to phenotypic selection (PS) to increase protein yield per unit area. Some 306 genotypes belonging to three connected recombinant inbred line (RIL) populations derived from paired crosses between elite cultivars were genotyped through genotyping-by-sequencing and phenotyped for grain yield and protein content on a dry matter basis in three autumn-sown environments of northern or central Italy. Line variation for mean protein content ranged from 21.7 to 26.6%. Purely genetic effects, compared with GEI effects, were over two-fold larger for protein content, and over 2-fold smaller for grain and protein yield per unit area. Grain yield and protein content exhibited no inverse genetic correlation. A genome-wide association study revealed a definite polygenic control not only for grain yield but also for protein content, with small amounts of trait variation accounted for by individual loci. On average, the GS predictive ability for individual RIL populations based on the rrBLUP model (which was selected out of four tested models) using by turns two environments for selection and one for validation was moderately high for protein content (0.53) and moderate for grain yield (0.40) and protein yield (0.41). These values were about halved for inter-environment, inter-population predictions using one RIL population for model construction to predict data of the other populations. The comparison between GS and PS for protein yield based on predicted gains per unit time and similar evaluation costs indicated an advantage of GS for model construction including the target RIL population and, in case of multi-year PS, even for model training based on data of a non-target population. In conclusion, protein content is less challenging than grain yield for phenotypic or genome-enabled improvement, and GS is promising for the simultaneous improvement of both traits.

Keywords: Pisum sativum; crop quality; crude protein yield; genetic variation; genomic selection; genotype × environment interaction; grain yield; inter-population prediction

DOI: https://doi.org/10.3389/fpls.2021.718713