bims-plasge 2020-04-19 papers

Issue of 2020–04–19
three papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Rice (N Y). 2020 Apr 15. 13(1): 25

OsSLC1 Encodes a Pentatricopeptide Repeat Protein Essential for Early Chloroplast Development and Seedling Survival.

Jun Lv, Lianguang Shang, Yun Chen, Yao Han, Xiaoyan Yang, Shuzhang Xie, Wenqin Bai, Mingyu Hu, Hong Wu, Kairong Lei, Ya'nan Yang, Shengzhen Ge, Hai Phuong Trinh, Yi Zhang, Longbiao Guo, Zhongwei Wang.

BACKGROUND: The large family of pentatricopeptide repeat (PPR) proteins is widely distributed among land plants. Such proteins play vital roles in intron splicing, RNA editing, RNA processing, RNA stability and RNA translation. However, only a small number of PPR genes have been identified in rice.
RESULTS: In this study, we raised a mutant from tissue-culture-derived plants of Oryza sativa subsp. japonica 'Zhonghua 11', which exhibited a lethal chlorosis phenotype from germination to the third-leaf stage. The mutant was designated seedling-lethal chlorosis 1 (slc1). The slc1 mutant leaves showed extremely low contents of photosynthetic pigments and abnormal chloroplast development, and were severely defective in photosynthesis. Map-based cloning of OsSLC1 revealed that a single base (G) deletion was detected in the first exon of Os06g0710800 in the slc1 mutant, which caused a premature stop codon. Knockout and complementation experiments further confirmed that OsSLC1 is responsible for the seedling-lethal chlorosis phenotype in the slc1 mutant. OsSLC1 was preferentially expressed in green leaves, and encoded a chloroplast-localized PPR protein harboring 12 PPR motifs. Loss-of-function of OsSLC1 affected the intron splicing of multiple group II introns, and especially precluded the intron splicing of rps16, and resulted in significant increase in the transcript levels of 3 chloroplast ribosomal RNAs and 16 chloroplast development-related and photosynthesis-related genes, and in significant reduction in the transcript levels of 1 chloroplast ribosomal RNAs and 2 chloroplast development-related and photosynthesis-related genes.
CONCLUSION: We characterized a novel chloroplast-localized PPR protein, OsSLC1, which plays a vital role in the intron splicing of multiple group II introns, especially the rps16 intron, and is essential for early chloroplast development and seedling survival in rice.

Keywords: Chloroplast development; Chlorosis phenotype; Intron splicing; Oryza sativa; PPR protein

DOI: https://doi.org/10.1186/s12284-020-00385-5

Theor Appl Genet. 2020 Apr 12.

The potential of hybrid breeding to enhance leaf rust and stripe rust resistance in wheat.

Ulrike Beukert, Guozheng Liu, Patrick Thorwarth, Philipp H G Boeven, C Friedrich H Longin, Yusheng Zhao, Martin Ganal, Albrecht Serfling, Frank Ordon, Jochen C Reif.

KEY MESSAGE: Hybrid wheat breeding is a promising strategy to improve the level of leaf rust and stripe rust resistance in wheat. Leaf rust and stripe rust belong to the most important fungal diseases in wheat production. Due to a dynamic development of new virulent races, epidemics appear in high frequency and causes significant losses in grain yield and quality. Therefore, research is needed to develop strategies to breed wheat varieties carrying highly efficient resistances. Stacking of dominant resistance genes through hybrid breeding is such an approach. Within this study, we investigated the genetic architecture of leaf rust and stripe rust resistance of 1750 wheat hybrids and their 230 parental lines using a genome-wide association study. We observed on average a lower rust susceptibility for hybrids in comparison to their parental inbred lines and some hybrids outperformed their better parent with up to 56%. Marker-trait associations were identified on chromosome 3D and 4A for leaf rust and on chromosome 2A, 2B, and 6A for stripe rust resistance by using a genome-wide association study with a Bonferroni-corrected threshold of P < 0.10. Detected loci on chromosomes 4A and 2A were located within previously reported genomic regions affecting leaf rust and stripe rust resistance, respectively. The degree of dominance was for most associations favorable in the direction of improved resistance. Thus, resistance can be increased in hybrid wheat breeding by fixing complementary leaf rust and stripe rust resistance genes with desired dominance effects in opposite parental pools.

DOI: https://doi.org/10.1007/s00122-020-03588-y

Genome Biol Evol. 2020 Apr 13. pii: evaa076. [Epub ahead of print]

Unprecedented intraindividual structural heteroplasmy in Eleocharis (Cyperaceae, Poales) plastomes.

Chaehee Lee, Tracey A Ruhlman, Robert K Jansen.

Plastid genomes (plastomes) of land plants have a conserved quadripartite structure in a gene dense unit-genome consisting of a large inverted repeat (IR) that separates two single copy regions. Recently, alternative plastome structures were suggested in Geraniaceae and in some conifers and Medicago the co-existence of inversion isomers has been noted. In this study, plastome sequences of two Cyperaceae, Eleocharis dulcis (water chestnut) and E. cellulosa (gulf coast spikerush), were completed. Unlike the conserved plastomes in basal groups of Poales, these Eleocharis plastomes have remarkably divergent features, including large plastome sizes, high rates of sequence rearrangements, low GC content and gene density, gene duplications and losses, and increased repetitive DNA sequences. A novel finding among these features was the unprecedented level of heteroplasmy with the presence of multiple plastome structural types within a single individual. Illumina paired-end assemblies combined with PacBio single-molecule real-time sequencing, long-range PCR and Sanger sequencing data, identified at least four different plastome structural types in both Eleocharis species. PacBio long read data suggested that one of the four E. dulcis plastome types predominates.

Keywords: RDR; chloroplast; homologous recombination; plastid genome; rearrangement; repeat

DOI: https://doi.org/10.1093/gbe/evaa076