Template-Type: ReDIF-Article 1.0 Author-Name: David VLK Author-Workplace-Name: Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic Author-Name: Jana ŘEPKOVÁ Title: Application of next-generation sequencing in plant breeding Abstract: In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping- by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture. Keywords: gene expression, marker-assisted selection, molecular marker, RNA-sequencing, SNP Journal: Czech Journal of Genetics and Plant Breeding Pages: 89-96 Volume: 53 Issue: 3 Year: 2017 DOI: 10.17221/192/2016-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/192/2016-CJGPB.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-201703-0001.txt Handle: RePEc:caa:jnlcjg:v:53:y:2017:i:3:id:192-2016-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Shuxia SUN Author-Workplace-Name: Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P.R. China Author-Workplace-Name: Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan Province, P.R. China Author-Name: LI Jing Author-Workplace-Name: Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P.R. China Author-Workplace-Name: Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan Province, P.R. China Author-Name: Dong CHEN Author-Workplace-Name: Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P.R. China Author-Workplace-Name: Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan Province, P.R. China Author-Name: Hongjiang XIE Author-Workplace-Name: Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P.R. China Author-Workplace-Name: Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan Province, P.R. China Author-Name: TU Meiyan Author-Workplace-Name: Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P.R. China Author-Workplace-Name: Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan Province, P.R. China Author-Name: Liu JIA Author-Workplace-Name: Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P.R. China Author-Workplace-Name: Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan Province, P.R. China Author-Name: Guoliang JIANG Author-Workplace-Name: Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P.R. China Title: Comparative transcriptomic analysis reveals a series of single nucleotide polymorphism between red- and white-fleshed loquats (Eriobotrya japonica) Abstract: Loquat (Eriobotrya japonica) is an economically important crop and red-fleshed cultivars have a much higher carotenoid content than white-fleshed cultivars. We used Illumina RNA-seq technology to gain a global overview of the loquat transcriptome from a mixture of fruit samples at different developmental stages for both red-fleshed and white-fleshed loquat. A total of 94.98 million paired-end short reads were obtained and 61 586 unigenes were generated from de novo assembly with an average length of 817 bp. Among these unigenes, 44 710 unigenes were annotated by blast against Nr, Swissprot, GO, COG and KEGG databases. For these annotated unigenes, 123 biosynthesis pathways were predicted by mapping these unigenes to the reference canonical pathways and 41 unigenes were predicted to be involved in carotenoid biosynthesis. RT-qPCR analysis showed that the expression level of the LCYB gene was higher in red-fleshed loquat and the CRTRB gene had a higher expression level in white-fleshed loquat. Comparative analysis of the two transcriptomes revealed 2396 single nucleotide polymorphisms (SNPs) between red- and white-fleshed loquats. The majority of SNPs identified between the two loquat cultivars were nonsense mutations and one out of eleven SNPs in candidate genes involved in carotenoid biosynthesis was a sense mutation. This suggests that the analysis based on transcriptomes can reveal key genes related to the carotenoid biosynthesis and more carotene in red-fleshed loquat cultivars may result from both more carotene produced by the higher expression of LCYB genes and less carotene converted because of the low expression of the CRTRB gene. All these results from the transcriptome analysis will be useful for the elucidation of genetic differences between red- and white-fleshed loquat fruits and further functional analysis for genes responsible for carotenoid accumulation. Keywords: carotenoid biosynthesis, expression analysis, SNP, transcriptome Journal: Czech Journal of Genetics and Plant Breeding Pages: 97-106 Volume: 53 Issue: 3 Year: 2017 DOI: 10.17221/43/2016-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/43/2016-CJGPB.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-201703-0002.txt Handle: RePEc:caa:jnlcjg:v:53:y:2017:i:3:id:43-2016-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Mehdi JOUDI Author-Workplace-Name: Meshkinshahr Faculty of Agriculture, University of Mohaghegh Ardabili, Ardabil, Iran Author-Name: Ali AHMADI Author-Workplace-Name: Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran Author-Name: Valiollah MOHAMMADI Author-Workplace-Name: Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran Title: Changes in stem and spike related traits resulting from breeding in Iranian wheat cultivars: associations with grain yield Abstract: This study investigated changes in stem and spike characteristics resulting from breeding in Iranian wheat cultivars, and their relationship with grain yield. Eighty-one wheat cultivars released between 1930 and 2006 were examined under well-watered (WW) and terminal drought stress (DS) conditions in Karaj during 2007-2008 and 2008-2009 and under WW condition at Parsabad in Moghan region during 2010-2011. A genetic improvement over time in stem specific weight (SSW) along with significant positive correlations between this trait and grain yield were found at Karaj under DS conditions and at Parsabad, suggesting that SSW could be used as an indirect selection criterion for yield in these environments. Time-dependent changes in spike dry weight showed that the magnitude of partitioned photoassimilates to the spike during the phase anthesis - 16 days after anthesis (16 DAA) was not changed by breeding. However, during the 16 DAA ‒ maturity phase, modern cultivars had more photoassimilates allocated to the spike than the old ones. This suggests that the sink is more limited during early grain growth than during the end of grain filling. Keywords: partitioned photoassimilates, sink limitation, stem specific weight, Triticum aestivum, Triticum durum Journal: Czech Journal of Genetics and Plant Breeding Pages: 107-113 Volume: 53 Issue: 3 Year: 2017 DOI: 10.17221/178/2016-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/178/2016-CJGPB.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-201703-0003.txt Handle: RePEc:caa:jnlcjg:v:53:y:2017:i:3:id:178-2016-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Wan Lin LI Author-Workplace-Name: Tuber and Crop Research Institute, Yunnan Agricultural University, Kunming, Yunnan, P.R. China Author-Name: Wen GUO Author-Workplace-Name: Tuber and Crop Research Institute, Yunnan Agricultural University, Kunming, Yunnan, P.R. China Author-Name: Ji Ping XIAO Author-Workplace-Name: Tuber and Crop Research Institute, Yunnan Agricultural University, Kunming, Yunnan, P.R. China Author-Name: Lei BAI Author-Workplace-Name: Tuber and Crop Research Institute, Yunnan Agricultural University, Kunming, Yunnan, P.R. China Author-Name: Hua Chun GUO Title: Germplasm evaluation and molecular selection of potato (Solanum tuberosum L.) cultivars with disease resistance in China Abstract: Foreground and background selections are two important aspects that need to be carefully considered by plant breeders during field selection. In this article, we used 7 disease resistance markers, including four late blight and three potato virus disease resistance gene markers, and 12 microsatellite markers to evaluate the disease resistance and genetic diversity of 76 potato cultivars in total which were collected from 15 provinces of China. The foreground selection results showed that a number of materials, clustered separately, contained more than two late blight resistance markers or pyramided late blight and virus disease resistance gene markers together. A lot of them were collected from the southwest of China. Additionally, the genetic backgrounds of all cultivars were relatively narrow and a limited number of cultivars (15.8%) contained both potato late blight and potato virus Y resistance markers. Also, only two accessions (Yunshu 103 and Lishu 7) contained both late blight and potato virus X resistance markers. In conclusion, this comprehensive evaluation of genetic resources will shed the light on potato disease resistance breeding in the future. Keywords: genetic diversity, potato late blight resistance, potato virus X resistance, potato virus Y resistance, SSR markers Journal: Czech Journal of Genetics and Plant Breeding Pages: 114-121 Volume: 53 Issue: 3 Year: 2017 DOI: 10.17221/101/2016-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/101/2016-CJGPB.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-201703-0004.txt Handle: RePEc:caa:jnlcjg:v:53:y:2017:i:3:id:101-2016-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Alena HANZALOVÁ Author-Workplace-Name: Department of Genetics and Plant Breeding Methods, Crop Research Institute, Prague-Ruzyně, Czech Republic Author-Name: Pavel BARTOŠ Author-Workplace-Name: Department of Genetics and Plant Breeding Methods, Crop Research Institute, Prague-Ruzyně, Czech Republic Author-Name: Taťána SUMÍKOVÁ Author-Workplace-Name: Department of Genetics and Plant Breeding Methods, Crop Research Institute, Prague-Ruzyně, Czech Republic Title: Pathotypes of wheat leaf rust (Puccinia triticina Eriks.) and resistance of registered cultivars in the Czech Republic in 2012-2015 Abstract: In 2012-2015 the virulence of the wheat leaf rust (Puccinia triticina Eriks.) population was studied on Thatcher near-isogenic lines with Lr1, Lr2a, Lr2b, Lr2c, Lr3a, Lr9, Lr10, Lr11, Lr13, Lr15, Lr17, Lr19, Lr21, Lr23, Lr24, Lr26 and Lr28. Samples of leaf rust were obtained from different parts of the Czech Republic. A total of 163 wheat leaf rust isolates were analysed. No virulence for the resistance gene Lr9 was found. Virulence for Lr19 was found only in one isolate in 2015. A lower frequency of virulence to Lr24, Lr2a, 2b, 2c and Lr28 was also observed. The presence of Lr10, Lr24, Lr26, Lr28 and Lr37 in registered cultivars was detected by polymerase chain reaction (PCR) molecular markers. Keywords: leaf rust pathotypes, Lr genes, resistance, wheat cultivars Journal: Czech Journal of Genetics and Plant Breeding Pages: 122-126 Volume: 53 Issue: 3 Year: 2017 DOI: 10.17221/121/2016-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/121/2016-CJGPB.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-201703-0005.txt Handle: RePEc:caa:jnlcjg:v:53:y:2017:i:3:id:121-2016-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Vladimíra SEDLÁKOVÁ Author-Workplace-Name: Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences in Prague, Prague, Czech Republic Author-Name: Petr SEDLÁK Author-Workplace-Name: Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences in Prague, Prague, Czech Republic Author-Name: Dukagjin ZEKA Author-Workplace-Name: Department of Crops, University of Prishtina, Prishtinë, Republic of Kosovo Author-Name: Jaroslava DOMKÁŘOVÁ Author-Workplace-Name: Department of Potato Genetic Resources and Author-Name: Petr DOLEŽAL Author-Workplace-Name: Department of Potato Protection, Potato Research Institute, Ltd., Havlíčkův Brod, Czech Republic Author-Name: Pavel VEJL Author-Workplace-Name: Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences in Prague, Prague, Czech Republic Title: Evaluation of variations in plastid DNA non-coding regions in selected species of the genus Solanum Abstract: The diversity of three non-coding plastid DNA loci (trnL/trnF spacer, trnV/16SrRNA spacer, trnL/trnL intron) was assessed in 16 Solanum L. species (135 individuals). Polymorphisms were detected by denaturing gradient gel electrophoresis (DGGE) and verified by direct sequencing. No intraspecific diversity and only poor interspecific diversity was detected. Unique S. mochiquense Ochoa specific length polymorphism at the trnL/trnL locus represented by duplication of an 18 bp segment was discovered. The detected DGGE interspecific trnL/trnF locus polymorphism did not specifically associate with single point mutations in the sequence confirmed by sequencing. The DGGE method was found to be a simple and cheap pre-exploring tool for mutation detection in compared DNA regions. Some identified polymorphisms can be used in the management of genetic resources. Keywords: DGGE, DNA sequencing, genetic diversity, point mutations, potato genetic resources Journal: Czech Journal of Genetics and Plant Breeding Pages: 127-131 Volume: 53 Issue: 3 Year: 2017 DOI: 10.17221/76/2015-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/76/2015-CJGPB.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-201703-0006.txt Handle: RePEc:caa:jnlcjg:v:53:y:2017:i:3:id:76-2015-CJGPB