bims-plasge 2019-04-28 papers

Issue of 2019–04–28
five papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Nat Commun. 2019 Apr 26. 10(1): 1949

Natural variation of OsGluA2 is involved in grain protein content regulation in rice.

Yihao Yang, Min Guo, Shengyuan Sun, Yelu Zou, Shuangyi Yin, Yannan Liu, Shuzhu Tang, Minghong Gu, Zefeng Yang, Changjie Yan.

Grain protein content (GPC) affects rice nutrition quality. Here, we identify two stable quantitative trait loci (QTLs), qGPC-1 and qGPC-10, controlling GPC in a mapping population derived from indica and japonica cultivars crossing. Map-based cloning reveals that OsGluA2, encoding a glutelin type-A2 precursor, is the candidate gene underlying qGPC-10. It functions as a positive regulator of GPC and has a pleiotropic effect on rice grain quality. One SNP located in OsGluA2 promoter region is associated with its transcript expression level and GPC diversity. Polymorphisms of this nucleotide can divide all haplotypes into low (OsGluA2LET) and high (OsGluA2HET) expression types. Population genetic and evolutionary analyses reveal that OsGluA2LET, mainly present in japonica accessions, originates from wild rice. However, OsGluA2HET, the dominant type in indica, is acquired through mutation of OsGluA2LET. Our results shed light on the understanding of natural variations of GPC between indica and japonica subspecies.

DOI: https://doi.org/10.1038/s41467-019-09919-y

J Exp Bot. 2019 Apr 25. pii: erz193. [Epub ahead of print]

Maize pentatricopeptide repeat protein DEK41 affects cis-splicing of mitochondrial nad4 intron 3 and seed development.

Chenguang Zhu, Guangpu Jin, Peng Fang, Yan Zhang, Xuzhen Feng, Yuanping Tang, Weiwei Qi, Rentao Song.

The splicing of organelle-encoded mRNA in plants requires nucleus-encoded proteins. The mechanism of organelle mRNA splicing and the factors involved in this process are not well understood. Pentatricopeptide repeat (PPR) proteins are known to participate in such RNA-protein interactions. Maize defective kernel 41 (dek41) is a seedling-lethal mutant that causes developmental defects. The Dek41 gene was cloned by Mu tag isolation and allelic confirmation, and was found to encode a P-type PPR protein that targets mitochondria. Mitochondrial RNA transcript profile analysis revealed that dek41 mutations cause reduced splicing efficiency of mitochondrial nad4 intron 3. Immature dek41 kernels exhibited severely reduced complex I assembly and NADH dehydrogenase activity. The up-regulated expression of alternative oxidase genes and deformed inner cristae of mitochondria in dek41, as revealed by transmission electron microscopy, indicate that proper splicing of nad4 is essential for mitochondrial functions and morphology. Consistent with this finding, differentially expressed genes in the dek41 endosperm included those related to mitochondrial function and activity. Our results indicate that DEK41 is a PPR protein affecting cis-splicing of mitochondrial nad4 intron 3 that is required for mitochondrial function and maize kernel development.

Keywords: Zea mays ; dek41 ; nad4 ; RNA splicing; mitochondria; pentatricopeptide repeat protein

DOI: https://doi.org/10.1093/jxb/erz193

Theor Appl Genet. 2019 Apr 24.

B-class MADS-box TM6 is a candidate gene for tomato male sterile-1526.

Xue Cao, Xiaoyan Liu, Xiaotian Wang, Mengxia Yang, Tong van Giang, Jing Wang, Xiaolin Liu, Shuai Sun, Kai Wei, Xiaoxuan Wang, Jianchang Gao, Yongchen Du, Yong Qin, Yanmei Guo, Zejun Huang.

KEY MESSAGE: Tomato male sterile-1526 locus was fine-mapped to an interval of 44.6 kb, and a B-class MADS-box gene TM6 was identified as the candidate gene. Male sterile lines have been widely used for hybrid seed production in many crop plants. The tomato male sterile-1526 (ms-1526) mutant displays abnormal stamens and exerted stigmas and is suitable for practical use. In this study, the ms-1526 locus was fine-mapped to a 44.6 kb interval that contained four putative genes. Thereinto, Solyc02g084630 encodes tomato B-class MADS-box gene TM6 (syn. TDR6), which plays an important role in stamen development. Sequencing revealed that there was a 12.7 kb deletion in the ms-1526 region, where the promoter and first four exons of the TM6 gene were absent. ms-1547, an allele of ms-1526, also contained the same deletion in the TM6 gene. And the other allele ms-15 mutant contained a single-nucleotide polymorphism (SNP, C to A) in the coding region of the TM6 gene, which led to a missense mutation (G to W). The codominant insertion/deletion (InDel) marker MS26D and codominant derived cleaved amplified polymorphic sequence (dCAPS) marker MS15C were developed based on the deletion and SNP, respectively. A real-time quantitative reverse-transcription PCR showed that expression of the TM6 gene was barely detectable in the flowers of the ms-1526 and ms-1547 mutants. In addition, other floral organ identity genes, pollen development marker genes, and pistil marker genes were differentially expressed between wild type and mutant flowers. These findings may facilitate functional analysis of the TM6 gene and help in the marker-assisted selection of ms-15 and its alleles in tomato breeding.

DOI: https://doi.org/10.1007/s00122-019-03342-z

Plant J. 2019 Apr 22.

Wheat ms5 male-sterility is induced by recessive homoeologous A and D genome non-specific Lipid Transfer Proteins.

Margaret A Pallotta, Patricia Warner, Allan Kouidri, Elise J Tucker, Mathieu Baes, Radoslaw Suchecki, Nathan Watson-Haigh, Takashi Okada, Melissa Garcia, Ajay Sandhu, Manjit Singh, Petra Wolters, Marc C Albertsen, A Mark Cigan, Ute Baumann, Ryan Whitford.

Nuclear male-sterile mutants with non-conditional, recessive and strictly monogenic inheritance are useful for both hybrid and conventional breeding systems and have long been a research focus for many crops. In allohexaploid wheat however, genic redundancy results in rarity of such mutants, with the EMS-induced mutant ms5 among the few reported to date. Here, we identify TaMs5 as a glycosylphosphatidylinositol anchored lipid transfer protein required for normal pollen exine development, and by transgenic complementation demonstrate that TaMs5-A restores fertility to ms5. We show ms5 locates to a centromere-proximal interval and has a sterility inheritance pattern modulated by TaMs5-D but not TaMs5-B. We describe two allelic forms of TaMs5-D, one of which is non-functional and confers monofactorial inheritance of sterility. The second form is functional but shows incomplete dominance. Consistent with reduced functionality, transcript abundance in developing anthers was found to be lower for TaMs5-D than TaMs5-A. At the 3B homoeolocus, we found only non-functional alleles among 178 diverse hexaploid and tetraploid wheats that include landraces and Triticum dicoccoides. Apparent ubiquity of non-functional TaMs5-B alleles suggests loss-of-function arose early in wheat evolution and therefore, at most, knockout of two homoeoloci is required for sterility. This work provides genetic information, resources and tools required for successful implementation of ms5 sterility in breeding systems for bread and durum wheats. This article is protected by copyright. All rights reserved.

Keywords: LTP ; Triticum aestivum ; ms5 ; Hybrid; genic; male-sterile; pollen; wheat

DOI: https://doi.org/10.1111/tpj.14350

Plant Cell. 2019 Apr 25. pii: tpc.00132.2019. [Epub ahead of print]

Leaf Variegation and Impaired Chloroplast Development Caused by a Truncated CCT Domain gene in albostrians Barley.

Mingjiu Li, Goetz Hensel, Martin Mascher, Michael Melzer, Nagaveni Budhagatapalli, Twan Rutten, Axel Himmelbach, Sebastian Beier, Viktor Korzun, Jochen Kumlehn, Thomas Boerner, Nils Stein.

Chloroplasts fuel plant development and growth by converting solar into chemical energy. They mature from proplastids through the concerted action of genes in both the organellar and the nuclear genome. Defects in such genes impair chloroplast development and may lead to pigment-deficient seedlings or seedlings with variegated leaves. Such mutants are instrumental as tools for dissecting genetic factors underlying the mechanisms involved in chloroplast biogenesis. Characterization of the green-white variegated albostrians mutant of barley has greatly broadened the field of chloroplast biology including the discovery of retrograde signaling. Here, we report identification of the ALBOSTRIANS gene HvAST by positional cloning as well as its functional validation based on independently induced mutants by TILLING and RNA-guided Cas9 endonuclease mediated gene editing. The phenotypes of the independent HvAST mutants imply residual activity of HvAST in the original albostrians allele conferring an imperfect penetrance of the variegated phenotype even at homozygous state of the mutation. HvAST is a homolog of the Arabidopsis thaliana CCT Motif transcription factor gene AtCIA2, which was reported to be involved in the expression of nuclear genes essential for chloroplast biogenesis. Interestingly, in barley we localized HvAST to the chloroplast indicating novel without any clear evidence of nuclear localization.

DOI: https://doi.org/10.1105/tpc.19.00132