bims-plasge 2019-11-10 papers

Issue of 2019–11–10
six papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Theor Appl Genet. 2019 Nov 06.

Two tightly linked genes coding for NAD-dependent malic enzyme and dynamin-related protein are associated with resistance to Cercospora leaf spot disease in cowpea (Vigna unguiculata (L.) Walp.).

Titnarong Heng, Akito Kaga, Xin Chen, Prakit Somta.

Cercospora leaf spot (CLS) caused by Cercospora canescens is an important disease of cowpea (Vigna unguiculata). A previous study using an F2 population [CSR12906 (susceptible) × IT90K-59-120 (resistant)] identified a major QTL qCLS9.1 for resistance to CLS. In this study, we finely mapped and identified candidate genes of qCLS9.1 using an F3:4 population of 699 individuals derived from two F2:3 individuals segregating at qCLS9.1 from the original population. Fine mapping narrowed down the qCLS9.1 for the resistance to a 60.6-Kb region on cowpea chromosome 10. There were two annotated genes in the 60.6-Kb region; Vigun10g019300 coding for NAD-dependent malic enzyme 1 (NAD-ME1) and Vigun10g019400 coding for dynamin-related protein 1C (DRP1C). DNA sequence analysis revealed 12 and 2 single nucleotide polymorphisms (SNPs) in the coding sequence (CDS) and the 5' untranslated region and TATA boxes of Vigun10g019300 and Vigun10g019400, respectively. Three SNPs caused amino acid changes in NAD-ME1 in CSR12906, N299S, S488N and S544N. Protein prediction analysis suggested that S488N of CSR12906 may have a deleterious effect on the function of NAD-ME1. Gene expression analysis demonstrated that IT90K-59-120 and CSR12906 challenged with C. canescens showed different expression in both Vigun10g019300 and Vigun10g019400. Taken together, these results indicated that Vigun10g019300 and Vigun10g019400 are the candidate genes for CLS resistance in the cowpea IT90K-59-120. Two derived cleaved amplified polymorphic sequence markers were developed to detect the resistance alleles at Vigun10g019300 and Vigun10g019400 in IT90K-59-120.

DOI: https://doi.org/10.1007/s00122-019-03470-6

Mol Plant. 2019 Oct 31. pii: S1674-2052(19)30336-3. [Epub ahead of print]

A Transcriptional Network Promotes Anthocyanin Biosynthesis in Tomato Flesh.

Chuanlong Sun, Lei Deng, Minmin Du, Jiuhai Zhao, Qian Chen, Tingting Huang, Hongling Jiang, Chang-Bao Li, Chuanyou Li.

Dietary anthocyanins are important health-promoting antioxidants that make a major contribution to the quality of fruits. It is intriguing that most tomato cultivars do not produce anthocyanins in fruit. However, the purple tomato variety Indigo Rose, which combines the dominant Aft locus and the recessive atv locus from wild tomato species, exhibits light-dependent anthocyanin accumulation in the skin. Here, we report that whereas Aft encodes a functional allele of an anthocyanin activator named SlAN2-like, atv encodes a non-functional allele of the anthocyanin repressor SlMYBATV. The expression of SlAN2-like is responsive to light and a functional SlAN2-like can activate both anthocyanin biosynthetic genes and their regulatory genes, suggesting that SlAN2-like acts as a master regulator and plays a critical role for the activation of anthocyanin biosynthesis. Our results reveal that cultivated tomatoes contain a non-functional allele of this master regulator and therefore fail to produce anthocyanins. Indeed, expression of a functional SlAN2-like in a tomato cultivar led to the activation of the entire anthocyanin biosynthesis pathway and high levels of anthocyanin accumulation in both peel and flesh. Our study exemplifies that efficient engineering of complex metabolic pathways could be achieved through tissue-specific expression of master transcriptional regulators.

Keywords: MBW complex; anthocyanin biosynthesis; master regulator; purple tomato; transcriptional regulation

DOI: https://doi.org/10.1016/j.molp.2019.10.010

Nat Plants. 2019 Nov 04.

A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history.

Michael F Scott, Laura R Botigué, Selina Brace, Chris J Stevens, Victoria E Mullin, Alice Stevenson, Mark G Thomas, Dorian Q Fuller, Richard Mott.

Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.

DOI: https://doi.org/10.1038/s41477-019-0534-5

Plants (Basel). 2019 Nov 06. pii: E475. [Epub ahead of print]8(11):

Two SNP Mutations Turned off Seed Shattering in Rice.

Yu Zhang, Jiawu Zhou, Ying Yang, Walid Hassan Elgamal, Peng Xu, Jing Li, Yasser Z El-Refaee, Suding Hao, Dayun Tao.

Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homozygous domestic haplotypes at one of the two sites, including 17 wild relatives of rice, 111 African cultivated rice and 65 Asian cultivated rice, showed the non-shattering phenotype. Dominant complementation of the G allele at G237T site and the C allele at C760T site in HS1 led to a hybrid shattering phenotype. These results help to shed light on the nature of seed shattering in rice during domestication and improve the moderate shattering varieties adapted to mechanized harvest.

Keywords: HS1; O. barthii; O. sativa; Seed shattering; haplotype

DOI: https://doi.org/10.3390/plants8110475

J Proteomics. 2019 Nov 05. pii: S1874-3919(19)30314-8. [Epub ahead of print] 103542

Proteomic dissection of the chloroplast: Moving beyond photosynthesis.

Nilesh Vikram Lande, Pragya Barua, Dipak Gayen, Sunil Kumar, Subhra Chakraborty, Niranjan Chakraborty.

Chloroplast, the photosynthetic machinery, converts photoenergy to ATP and NADPH, which powers the production of carbohydrates from atmospheric CO2 and H2O. It also serves as a major production site of multivariate pro-defense molecules, and coordinate with other organelles for cell defense. Chloroplast harbors 30-50% of total cellular proteins, out of which 80% are membrane residents and are difficult to solubilize. While proteome profiling has illuminated vast areas of biological protein space, a great deal of effort must be invested to understand the proteomic landscape of the chloroplast, which plays central role in photosynthesis, energy metabolism and stress-adaptation. Therefore, characterization of chloroplast proteome would not only provide the foundation for future investigation of expression and function of chloroplast proteins, but would open up new avenues for modulation of plant productivity through synchronizing chloroplastic key components. In this review, we summarize the progress that has been made to build new understanding of the chloroplast proteome and implications of chloroplast dynamicsing generate metabolic energy and modulating stress adaptation.

Keywords: Chloroplast; Differentially accumulated proteins; Kranz regulators; Photosynthetic machinery; Proteome landscape; Stress adaptation

DOI: https://doi.org/10.1016/j.jprot.2019.103542

Int J Mol Sci. 2019 Nov 07. pii: E5562. [Epub ahead of print]20(22):

Functional Dissection of the Chickpea (Cicer arietinum L.) Stay-Green Phenotype Associated with Molecular Variation at an Ortholog of Mendel's I Gene for Cotyledon Color: Implications for Crop Production and Carotenoid Biofortification.

"Stay-green" crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its potential use for improvement of chickpea environmental adaptations and nutritional value. We examined 40 stay-green accessions and a set of 29 BC2F4-5 stay-green introgression lines using a stay-green donor parent ICC 16340 and two Indian elite cultivars (KAK2, JGK1) as recurrent parents. Genetic studies of segregating populations indicated that the green cotyledon trait is controlled by a single recessive gene that is invariantly associated with the delayed degreening (extended chlorophyll retention). We found that the chickpea ortholog of Mendel's I locus of garden pea, encoding a SGR protein as very likely to underlie the persistently green cotyledon color phenotype of chickpea. Further sequence characterization of this chickpea ortholog CaStGR1 (CaStGR1, for carietinum stay-green gene 1) revealed the presence of five different molecular variants (alleles), each of which is likely a loss-of-function of the chickpea protein (CaStGR1) involved in chlorophyll catabolism. We tested the wild type and green cotyledon lines for components of adaptations to dry environments and traits linked to agronomic performance in different experimental systems and different levels of water availability. We found that the plant processes linked to disrupted CaStGR1 gene did not functionality affect transpiration efficiency or water usage. Photosynthetic pigments in grains, including provitaminogenic carotenoids important for human nutrition, were 2-3-fold higher in the stay-green type. Agronomic performance did not appear to be correlated with the presence/absence of the stay-green allele. We conclude that allelic variation in chickpea CaStGR1 does not compromise traits linked to environmental adaptation and agronomic performance, and is a promising genetic technology for biofortification of provitaminogenic carotenoids in chickpea.

Keywords: Cicer arietinum; Mendel’s I gene; biofortification; carotenoids; chickpea; cosmetic stay-green; green cotyledon; pro-vitamin A

DOI: https://doi.org/10.3390/ijms20225562