bims-plasge 2019-10-20 papers

Issue of 2019–10–20
four papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Theor Appl Genet. 2019 Oct 17.

Transcriptomics, chromosome engineering and mapping identify a restorer-of-fertility region in the CMS wheat system msH1.

Cristina Rodríguez-Suárez, Paolo Bagnaresi, Luigi Cattivelli, Fernando Pistón, Almudena Castillo, Azahara C Martín, Sergio G Atienza, Carmen Ramírez, Antonio Martín.

KEY MESSAGE: An original RNA-seq mapping strategy, validated with chromosome engineering and physical mapping, identifies candidate genes for fertility restoration in the 6HchS chromosome of Hordeum chilense in the wheat msH1 system. Cytoplasmic male sterility (CMS) is a valuable trait for hybrid seed production. The msH1 CMS system in common wheat results from the incompatibility between the nuclear genome of wheat and the cytoplasm of the wild barley Hordeum chilense. This work aims to identify H. chilense candidate genes for fertility restoration in the msH1 system with a multidisciplinary strategy based on chromosome engineering, differential expression analysis and genome mapping. Alloplasmic isogenic wheat lines differing for fertility, associated with the presence of an acrocentric chromosome Hchac resulting from the rearrangement of the short arms of H. chilense chromosomes 1Hch and 6Hch, were used for transcriptome sequencing. Two novel RNA-seq mapping approaches were designed and compared to identify differentially expressed genes of H. chilense associated with male fertility restoration. Minichromosomes (Hchmi), new smaller reorganizations of the Hchac also restoring fertility, were obtained and used to validate the candidate genes. This strategy was successful identifying a putative restorer-of-fertility region on 6HchS, with six candidate genes, including the ortholog of the barley restorer gene Rfm1. Additionally, transcriptomics gave preliminary insights on sterility and restoration networks showing the importance of energy supply, stress, protein metabolism and RNA processing.

Keywords: Common wheat; Cytoplasmic male sterility; Hordeum chilense; Minichromosomes; RNA-seq; Restorer-of-fertility

DOI: https://doi.org/10.1007/s00122-019-03457-3

Trends Plant Sci. 2019 Oct 11. pii: S1360-1385(19)30218-3. [Epub ahead of print]

Molecular Basis of Pollen Germination in Cereals.

Yu-Jin Kim, Dabing Zhang, Ki-Hong Jung.

Understanding the molecular basis of pollen germination in cereals holds great potential to improve yield. Pollen, a highly specialized haploid male gametophyte, transports sperm cells through a pollen tube to the female ovule for fertilization, directly determining grain yield in cereal crops. Although insights into the regulation of pollen germination and gamete interaction have advanced rapidly in the model Arabidopsis thaliana (arabidopsis), the molecular mechanisms in monocot cereals remain largely unknown. Recently, pollen-specific genome-wide and mutant analyses in rice and maize have extended our understanding of monocot regulatory components. We highlight conserved and diverse mechanisms underlying pollen hydration, germination, and tube growth in cereals that provide ideas for translating this research from arabidopsis. Recent developments in gene-editing systems may facilitate further functional genetic research.

Keywords: cereals; hydration; maize; pollen germination; pollen tube; rice

DOI: https://doi.org/10.1016/j.tplants.2019.08.005

Plant Reprod. 2019 Oct 16.

Molecular mapping of a novel male-sterile gene msNJ in soybean [Glycine max (L.) Merr.].

Zhixing Nie, Tuanjie Zhao, Meifeng Liu, Jinying Dai, Tingting He, Duo Lyu, Jinming Zhao, Shouping Yang, Junyi Gai.

Nuclear male sterility (NMS) is a potential characteristic in crop recurrent selection and hybrid breeding. Mapping of nuclear male-sterile genes is key to utilizing NMS. Previously, we discovered a spontaneous soybean (Glycine max [L.] Merr.) male-sterile female-fertile mutant NJS-13H, which was conferred by a single recessive gene, designated msNJ. In this study, the msNJ was mapped to Chromosome 10 (LG O), and narrowed down between two SSR (simple sequence repeats) markers, BARCSOYSSR_10_794 and BARCSOYSSR_10_819 using three heterozygote-derived segregating populations, i.e., (NJS-13H × NN1138-2)F2, (NJS-13H × N2899)F2 and (NJS-13H)SPAG (segregating populations in advanced generations). This region spans approximately 1.32 Mb, where 27 genes were annotated according to the soybean reference genome sequence (Wm82.a2.v1). Among them, four genes were recognized as candidate genes for msNJ. Comparing to the physical locations of all the known male-sterile loci, msNJ is demonstrated to be a new male-sterile locus. This result may help the utilization and cloning of the gene.

Keywords: Gene mapping; Nuclear male sterility (NMS); Simple sequence repeats (SSR); Soybean [Glycine max (L.) Merr.]

DOI: https://doi.org/10.1007/s00497-019-00377-6

Theor Appl Genet. 2019 Oct 17.

An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the liy short fiber phenotype in cotton.

David D Fang, Marina Naoumkina, Gregory N Thyssen, Efrem Bechere, Ping Li, Christopher B Florane.

KEY MESSAGE: The EMS-induced threonine/isoleucine substitution in a tetratricopeptide repeat-like superfamily protein encoded by gene Ghir_A12G008870 is responsible for the Ligon-lintless-y (liy) short fiber phenotype in cotton. A short fiber mutant Ligon-lintless-y was created through treating the seeds of the cotton line MD15 with ethyl methanesulfonate. Genetic analysis indicated that the short fiber phenotype is controlled by a single recessive locus designated liy. From F2 populations derived from crosses between the mutant and its wild type (WT), we selected 132 short fiber progeny (liy/liy) and made two DNA bulks. We sequenced these DNA bulks along with the two parents of the population. The liy locus was located on chromosome A12. Using multiple F2 populations and F3 progeny plants, we mapped the liy locus within a genomic region of 1.18 Mb. In this region, there is only one gene, i.e., Ghir_A12G008870 encoding a tetratricopeptide repeat-like superfamily protein that has a non-synonymous mutation between the liy mutant and its WT. Analysis of a SNP marker representing this gene in the F2 and F3 progeny plants demonstrated its complete linkage with the liy short fiber phenotype. We further analyzed this SNP marker in a panel of 384 cotton varieties. The mutant allele is absent in all varieties analyzed. RNAseq and RT-qPCR analysis of the gene Ghir_A12G008870 during fiber development showed a significant expression difference between the liy mutant and its WT in developing fiber cells beginning at 12 days post-anthesis. Virus-induced gene silencing of the gene Ghir_A12G008870 significantly reduced the fiber length of the WT cotton line MD15. Taken together, our results suggest that the gene Ghir_A12G008870 is involved in the cotton fiber cell elongation process and is a promising candidate gene responsible for the liy short fiber phenotype.

Keywords: Cotton; EMS; Ligon-lintless-y mutation; Mapping-by-sequencing; Short fiber mutation; Tetratricopeptide repeat (TPR)-like superfamily protein

DOI: https://doi.org/10.1007/s00122-019-03456-4