bims-pisump 2018-06-24 papers

Issue of 2018–06–24
four papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Theor Appl Genet. 2018 Jun 16.

A bean common mosaic virus (BCMV)-resistance gene is fine-mapped to the same region as Rsv1-h in the soybean cultivar Suweon 97.

Mian Wu, Wen-Ping Wu, Cheng-Chen Liu, Ying-Na Liu, Xiao-Yi Wu, Fang-Fang Ma, An-Qi Zhu, Jia-Yin Yang, Bin Wang, Jian-Qun Chen.

KEY MESSAGE: In the soybean cultivar Suweon 97, BCMV-resistance gene was fine-mapped to a 58.1-kb region co-localizing with the Soybean mosaic virus (SMV)-resistance gene, Rsv1-h raising a possibility that the same gene is utilized against both viral pathogens. Certain soybean cultivars exhibit resistance against soybean mosaic virus (SMV) or bean common mosaic virus (BCMV). Although several SMV-resistance loci have been reported, the understanding of the mechanism underlying BCMV resistance in soybean is limited. Here, by crossing a resistant cultivar Suweon 97 with a susceptible cultivar Williams 82 and inoculating 220 F2 individuals with a BCMV strain (HZZB011), we observed a 3:1 (resistant/susceptible) segregation ratio, suggesting that Suweon 97 possesses a single dominant resistance gene against BCMV. By performing bulked segregant analysis with 186 polymorphic simple sequence repeat (SSR) markers across the genome, the resistance gene was determined to be linked with marker BARSOYSSR_13_1109. Examining the genotypes of nearby SSR markers on all 220 F2 individuals then narrowed down the gene between markers BARSOYSSR_13_1109 and BARSOYSSR_13_1122. Furthermore, 14 previously established F2:3 lines showing crossovers between the two markers were assayed for their phenotypes upon BCMV inoculation. By developing six more SNP (single nucleotide polymorphism) markers, the resistance gene was finally delimited to a 58.1-kb interval flanked by BARSOYSSR_13_1114 and SNP-49. Five genes were annotated in this interval of the Williams 82 genome, including a characteristic coiled-coil nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR, CNL)-type of resistance gene, Glyma13g184800. Coincidentally, the SMV-resistance allele Rsv1-h was previously mapped to almost the same region, thereby suggesting that soybean Suweon 97 likely relies on the same CNL-type R gene to resist both viral pathogens.

DOI: https://doi.org/10.1007/s00122-018-3117-3

Theor Appl Genet. 2018 Jun 16.

Comparative genome-wide mapping versus extreme pool-genotyping and development of diagnostic SNP markers linked to QTL for adult plant resistance to stripe rust in common wheat.

Jianhui Wu, Shuo Huang, Qingdong Zeng, Shengjie Liu, Qilin Wang, Jingmei Mu, Shizhou Yu, Dejun Han, Zhensheng Kang.

KEY MESSAGE: A major stripe rust resistance QTL on chromosome 4BL was localized to a 4.5-Mb interval using comparative QTL mapping methods and validated in 276 wheat genotypes by haplotype analysis. CYMMIT-derived wheat line P10103 was previously identified to have adult plant resistance (APR) to stripe rust in the greenhouse and field. The conventional approach for QTL mapping in common wheat is laborious. Here, we performed QTL detection of APR using a combination of genome-wide scanning and extreme pool-genotyping. SNP-based genetic maps were constructed using the Wheat55 K SNP array to genotype a recombinant inbred line (RIL) population derived from the cross Mingxian 169 × P10103. Five stable QTL were detected across multiple environments. A fter comparing SNP profiles from contrasting, extreme DNA pools of RILs six putative QTL were located to approximate chromosome positions. A major QTL on chromosome 4B was identified in F2:4 contrasting pools from cross Zhengmai 9023 × P10103. A consensus QTL (LOD = 26-40, PVE = 42-55%), named QYr.nwafu-4BL, was defined and localized to a 4.5-Mb interval flanked by SNP markers AX-110963704 and AX-110519862 in chromosome arm 4BL. Based on stripe rust response, marker genotypes, pedigree analysis and mapping data, QYr.nwafu-4BL is likely to be a new APR QTL. The applicability of the SNP-based markers flanking QYr.nwafu-4BL was validated on a diversity panel of 276 wheat lines. The additional minor QTL on chromosomes 4A, 5A, 5B and 6A enhanced the level of resistance conferred by QYr.nwafu-4BL. Marker-assisted pyramiding of QYr.nwafu-4BL and other favorable minor QTL in new wheat cultivars should improve the level of APR to stripe rust.

DOI: https://doi.org/10.1007/s00122-018-3113-7

Gene. 2018 Jun 13. pii: S0378-1119(18)30683-8. [Epub ahead of print]

Genome-wide analysis of maize CONSTANS-LIKE gene family and expression profiling under light/dark and abscisic acid treatment.

Nannan Song, Zhilan Xu, Jing Wang, Qianqian Qin, Haiyang Jiang, Weina Si, Xiaoyu Li.

The CONSTANS-LIKE (COL) gene has an important role both in regulation flowering through photoperiodic control and response to abiotic stress. In the present study, we performed a genome-wide analysis of maize COL gene family and identified 19 non-redundant ZmCOL genes, which were unequally distributed on ten maize chromosomes. Analysis of compound phylogenetic tree (maize, sorghum, rice and Arabidopsis) showed high bootstrap, as well as conserved domain and semblable gene structures among members within the same clade, revealing that COL genes in same clade were from the common ancestral and prior to the divergence of monocots and dicots lineages. Calculation of Ka/Ks ratio demonstrated that most duplicated ZmCOLs experienced purifying selection, which suggested limited functional divergence after duplication events. Comparing interspecies gene collinearity between three major grasses species, extensive microsynteny was detected among maize, sorghum and rice COL-containing segments. Additionally, several light-responsive and one ABA-responsive cis-elements could be detected for ZmCOL genes in group A. Therefore, qRT-PCR was performed to explore the expression patterns of ZmCOL genes in group A under light/dark conditions and ABA treatment. Our results laid the foundation for functional characterization of ZmCOL proteins and uncovering the biological roles of COL genes in response to stress in future.

Keywords: ABA stress; CONSTANS-LIKE gene (COL); Genome-wide analysis; Light regulation; Maize; Microsynteny analysis

DOI: https://doi.org/10.1016/j.gene.2018.06.032

Plant Physiol Biochem. 2018 Jun 04. pii: S0981-9428(18)30253-5. [Epub ahead of print]129 285-294

Initial characterization of newly identified mitochondrial and chloroplast small HSPs from sugarcane shows that these chaperones have different oligomerization states and substrate specificities.

Glaucia M S Pinheiro, Carlos H I Ramos.

Chaperones belonging to the small heat shock protein (sHSP) family are ubiquitous and exhibit elevated expression under stresses conditions to protect proteins against aggregation, thereby contributing to the stress tolerance of the organism. Tropical plants are constantly exposed to high temperatures, and the mechanisms by which these plants tolerate heat stress are of foremost importance to basic science as well as applied agrobiotechnology. Therefore, this study aims to characterize sHSPs from different organelles from sugarcane, an important crop that is associated with sugar and bioenergy production. An expression sequence tag database of sugarcane was searched, and sHsp genes of mitochondrial and chloroplast organelles were selected and cloned. The proteins were expressed in Escherichia coli and isolated and purified by two chromatographic steps with high purity as single species. Circular dichroism and fluorescence spectroscopy showed that both proteins were purified in their folded states with a predominant β-sheet secondary structure. Determination of the molecular weight, diffusion coefficient and Stokes radius parameters showed that both chaperones form large spherical-like oligomers in solution. The two sHSPs had different oligomeric states and substrate specificities. The mitochondrial sHSP was a 20-mer with ability to protect model substrates that differ from that of the 16-meric sHSP from chloroplasts. These results indicate that both sHSPs are key agents to protect against stress confirming the importance of the great diversity of sHSP chaperones in plants for homeostasis maintenance. Moreover, to our knowledge, this is the first report about small HSPs from sugarcane organelles.

Keywords: Chaperone activity; Chloroplast; Mitochondria; Proteostasis; Small heat shock proteins; Sugarcane

DOI: https://doi.org/10.1016/j.plaphy.2018.06.002