bims-plasge 2019-07-07 papers

J Exp Bot. 2019 Jun 28. pii: erz305. [Epub ahead of print]

PPR-SMR1 is required for the splicing of multiple mitochondrial introns and interacts with Zm-mCSF1 and is essential for seed development in maize.

Zongliang Chen, Hong-Chun Wang, Jiayu Shen, Feng Sun, Miaodi Wang, Chunhui Xu, Bao-Cai Tan.

Group II introns are ribozymes that can excise themselves from precursor-RNA transcripts, but plant organellar group II introns have sustained structural deviations that inhibit ribozyme activity. Thus, splicing of these introns requires the assistance of nuclear- and/or organellar-encoded splicing factors. But how these splicing factors function remains unclear. Here we report the functions and interactions of two splicing factors, PPR-SMR1 and Zm-mCSF1, in intron splicing in maize mitochondria. PPR-SMR1 is a SMR domain-containing PPR protein, and Zm-mCSF1, a CRM domain-containing protein. Both proteins are targeted to mitochondria. Loss-of-function mutations in each of them severely arrest embryogenesis and endosperm development in maize. Functional analyses indicate that PPR-SMR1 and Zm-mCSF1 are required for the splicing of most mitochondrial group II introns. Among them, nad2-intron 2 and 3, and nad5-intron 1 are PPR-SMR1/Zm-mCSF1-dependent introns. Furthermore, protein interaction assays suggest that PPR-SMR1 can interact with Zm-mCSF1 through its N-terminus, and Zm-mCSF1 is a self-interacting protein. These findings suggest that PPR-SMR1, a novel splicing factor, acts in the splicing of multiple group II introns in maize mitochondria, and the protein-protein interaction between PPR-SMR1 and Zm-mCSF1 might allow the formation of large macromolecular splicing complexes in maize mitochondria.

Keywords: Group II introns; Maize; Mitochondria; Organelle Biogenesis; PPR Proteins; Seed Development

DOI: https://doi.org/10.1093/jxb/erz305

Theor Appl Genet. 2019 Jun 28.

Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping.

Saarah Kuzay, Yunfeng Xu, Junli Zhang, Andrew Katz, Stephen Pearce, Zhenqi Su, Max Fraser, James A Anderson, Gina Brown-Guedira, Noah DeWitt, Amanda Peters Haugrud, Justin D Faris, Eduard Akhunov, Guihua Bai, Jorge Dubcovsky.

KEY MESSAGE: A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a promising candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families ( > 10,000 plants) from two crosses to map the 7AL QTL to an 87-kb region (674,019,191-674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high-SNS allele in both H1 × H2 and H2 × H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~ 1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A02G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.

DOI: https://doi.org/10.1007/s00122-019-03382-5

Mol Phylogenet Evol. 2019 Jun 25. pii: S1055-7903(19)30175-7. [Epub ahead of print]139 106540

Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.

Yun-Xia Li, Zhang-Hai Li, Andre Schuitman, Mark W Chase, Jian-Wu Li, Wei-Chang Huang, Arief Hidayat, Sha-Sha Wu, Xiao-Hua Jin.

To advance our knowledge of orchid relationships and timing of their relative divergence, we used 76 protein-coding genes from plastomes (ptCDS) and 38 protein-coding genes from mitochondrial genomes (mtCDS) of 74 orchids representing the five subfamilies and 18 tribes of Orchidaceae, to reconstruct the phylogeny and temporal evolution of the Orchidaceae. In our results, the backbone of orchid tree well supported with both datasets, but there are conflicts between these trees. The phylogenetic positions of two subfamilies (Vanilloideae and Cypripedioideae) are reversed in these two analyses. The phylogenetic positions of several tribes and subtribes, such as Epipogiinae, Gastrodieae, Nerviliinae, and Tropidieae, are well resolved in mtCDS tree. Thaieae have a different position among higher Epidendroideae, instead of sister to the higher Epidendroideae. Interrelationships of several recently radiated tribes within Epidendroideae, including Vandeae, Collabieae, Cymbidieae, Epidendreae, Podochileae, and Vandeae, have good support in the ptCDS tree, but most are not resolved in the mtCDS tree. Conflicts between the two datasets may be attributed to the different substitution rates in these two genomes and heterogeneity of substitution rate of plastome. Molecular dating indicated that the first three subfamilies, Apostasioideae, Cypripedioideae and Vanilloideae, diverged relatively quickly, and then there was a longer period before the last two subfamilies, Orchidoideae and Epidendroideae, began to radiate. Most mycoheterotrophic clades of Orchidaceae evolved in the last 30 million years with the exception of Gastrodieae.

Keywords: Cypripedioideae; Mitochondrial genome; Mycoheterotrophic orchids; Orchidaceae; Plastid genome; Vanilloideae

DOI: https://doi.org/10.1016/j.ympev.2019.106540

PLoS One. 2019 ;14(6): e0218526

Diversity of a wall-associated kinase gene in wild and cultivated barley.

Beata I Czajkowska, Glynis Jones, Terence A Brown.

Domestication of barley and other cereals was accompanied by an increase in seed size which has been ascribed to human selection, large seeds being preferred by early farmers or favoured by cultivation practices such as deep sowing. An alternative suggestion is that the increase in seed size was an indirect consequence of selection for plants with more vigorous growth. To begin to address the latter hypothesis we studied the diversity of HvWAK1, a wall-associated kinase gene involved in root proliferation, in 220 wild barley accessions and 200 domesticated landraces. A 3655-bp sequence comprising the gene and upstream region contained 69 single nucleotide polymorphisms (SNPs), one indel and four short tandem repeats. A network of 50 haplotypes revealed a complex evolutionary relationship, but with landraces largely restricted to two parts of the topology. SNPs in the HvWAK1 coding region resulted in nonsynonymous substitutions at nine positions in the translation product, but none of these changes were predicted to have a significant effect on the protein structure. In contrast, the region upstream of the coding sequence contained five SNPs that were invariant in the domesticated population, fixation of these SNPs decreasing the likelihood that the upstream of a pair of TATA boxes and transcription start sites would be used to promote transcription of HvWAK1. The sequence diversity therefore suggests that the cis-regulatory region of HvWAK1 might have been subject to selection during barley domestication. The extent of root proliferation has been linked with traits such as above-ground biomass, so selection for particular cis-regulatory variants of HvWAK1 would be consistent with the hypothesis that seed size increases during domestication were the indirect consequence of selection for plants with increased growth vigour.

DOI: https://doi.org/10.1371/journal.pone.0218526

J Exp Bot. 2019 Jul 03. pii: erz312. [Epub ahead of print]

A CC-NBS-LRR Gene Induces Hybrid Lethality in Cotton.

Jieqiong Deng, Lei Fang, Xiefei Zhu, Baoliang Zhou, Tianzhen Zhang.

Hybrid lethality as a reproductive barrier has been found in many eukaryotes. Most hybrid lethality cases follow the Bateson-Dobzhansky-Muller genetic incompatibility model, involving two or more loci. Here we report that a coiled coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) gene is the causal gene underlying the Le4 locus for interspecific hybrid lethality between Gossypium barbadense and G. hirsutum. Silencing this CC-NBS-LRR gene can restore F1 plants from a lethal to a normal phenotype. A total of 11,099 genes were differentially expressed between the normal and lethal F1 plant leaves. Of them, autoimmune response related genes were highly enriched. ATP-binding and ATPase related genes were up-regulated before the lethal syndrome appeared; this may result in the conversion of Le4 into an active state and, thus, triggering immune signals without biotic/abiotic stress. The evolution and domestication of Sea Island cottons and the molecular mechanisms of hybrid lethality associated with autoimmune responses are discussed in relation to our findings. These findings bring new insights into reproductive isolation and may benefit cotton breeding.

Keywords: ATP-binding; Cotton; DNA-dependent ATPase activity; Hybrid lethality; Map-based cloning; NBS-LRR genes; autoimmunity response

DOI: https://doi.org/10.1093/jxb/erz312