Genomes and Genes
Summary: The purposeful manipulation of plant species with the goal of creating desired genotypes and phenotypes, using techniques such as controlled pollination and or genetic engineering, followed by artificial selection of progeny.
- Shandil R, Chakrabarti S, Singh B, Sharma S, Sundaresha S, Kaushik S, et al. Genotypic background of the recipient plant is crucial for conferring RB gene mediated late blight resistance in potato. BMC Genet. 2017;18:22 pubmed publisher..Besides, it also corroborates the fact that efficacy of R gene is not solely dependent on its presence in the variety but largely depends on the genetic background of the recipient genotype. ..
- Okada S, Suehiro M, Ebana K, Hori K, Onogi A, Iwata H, et al. Genetic dissection of grain traits in Yamadanishiki, an excellent sake-brewing rice cultivar. Theor Appl Genet. 2017;130:2567-2585 pubmed publisher..These data can be informative for programs involved in breeding better cooking and brewing rice cultivars. ..
- Ovenden B, Milgate A, Lisle C, Wade L, Rebetzke G, Holland J. Selection for water-soluble carbohydrate accumulation and investigation of genetic × environment interactions in an elite wheat breeding population. Theor Appl Genet. 2017;130:2445-2461 pubmed publisher..However, correlations between grain yield and WSCC or WSCA were weak and variable, suggesting that selection for these traits is not a better strategy for improving yield under drought than direct selection for yield. ..
- Li J, Wang D, Xu X, Bai L, Peng B, Pu Y, et al. Utilization of UPLC/Q-TOF-MS-Based Metabolomics and AFLP-Based Marker-Assisted Selection to Facilitate/Assist Conventional Breeding of Polygala tenuifolia. Chem Biodivers. 2017;14: pubmed publisher..The proposed method of metabolomics coupled with MAS could facilitate/assist the breeding of P. tenuifolia. ..
- Bernal Vasquez A, Gordillo A, Schmidt M, Piepho H. Genomic prediction in early selection stages using multi-year data in a hybrid rye breeding program. BMC Genet. 2017;18:51 pubmed publisher..The models were evaluated under different scenarios reflecting common practice in plant breeding programs, such as different degrees of relatedness between training and validation sets, and using a selected ..
- Dantas S, Silva F, Silva L, Silva F. Strategy for selection of soybean genotypes tolerant to drought during germination. Genet Mol Res. 2017;16: pubmed publisher..2 MPa was efficient for selecting soybean cultivars tolerant to water stress. This was accomplished by evaluating the percentage of germination, along with variables related to the dynamics of reservation. ..
- Wang Z, Cao H, Wu L, Guo Y, Mei Q, Li M, et al. A set of novel microsatellite markers developed for an economically important tree, Dracontomelon duperreanum, in China. Genet Mol Res. 2017;16: pubmed publisher..These microsatellite markers will be valuable for studying the genetic diversities and structures in D. duperreanum and other Dracontomelon species. ..
- Costa J, Fracetto G, Fracetto F, Santos M, Lira Júnior M. Genetic diversity of Desmanthus sp accessions using ISSR markers and morphological traits. Genet Mol Res. 2017;16: pubmed publisher..Our findings showed that 17L, 27L, 25F, 22F, 19S, 13Au, and 28G accessions could be used in breeding programs to explore the maximum genetic divergence. ..
- Leisner C, Kamileen M, Conway M, O Connor S, Buell C. Differential iridoid production as revealed by a diversity panel of 84 cultivated and wild blueberry species. PLoS ONE. 2017;12:e0179417 pubmed publisher..Taken together, this data provides the foundation to dissect the molecular and genetic basis of iridoid production in blueberry. ..
- Yuan Y, Zhang Q, Zeng S, Gu L, Si W, Zhang X, et al. Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars. BMC Genomics. 2017;18:307 pubmed publisher..Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes. ..
- Hirut B, Shimelis H, Fentahun M, Bonierbale M, Gastelo M, Asfaw A. Combining ability of highland tropic adapted potato for tuber yield and yield components under drought. PLoS ONE. 2017;12:e0181541 pubmed publisher..The new population is shown to be a valuable genetic resource for variety selection and improvement of potato's adaptation to the drought prone areas in northwest Ethiopia and similar environments. ..
- Thorwarth P, Ahlemeyer J, Bochard A, Krumnacker K, Blümel H, Laubach E, et al. Genomic prediction ability for yield-related traits in German winter barley elite material. Theor Appl Genet. 2017;130:1669-1683 pubmed publisher..Our work contributes to designing long-term genetic prediction programs for barley breeding. ..
- Díaz B, Argollo D, Franco M, Nucci S, Siqueira W, de Laat D, et al. High genetic diversity of Jatropha curcas assessed by ISSR. Genet Mol Res. 2017;16: pubmed publisher..Nei's genetic distance between groups was 0.14. The results showed the importance of Mexican accessions, congeneric wild species, and interspecific hybrids for conservation and development of new genotypes in breeding programs. ..
- Rincent R, Charcosset A, Moreau L. Predicting genomic selection efficiency to optimize calibration set and to assess prediction accuracy in highly structured populations. Theor Appl Genet. 2017;130:2231-2247 pubmed publisher..We illustrated that the CD criteria could be adapted to various prediction scenarios including inter and intra-family predictions, resulting in higher prediction accuracies. ..
- Pereira A, De Almeida A, Branco M, Costa M, Ahnert D. Combining ability, heritability and genotypic relations of different physiological traits in cacao hybrids. PLoS ONE. 2017;12:e0178790 pubmed publisher..Additionally, plants with higher carbon fixation, better water use, higher carboxylation efficiency and greater magnesium accumulation in leaves can be selected. ..
- Schaefer H, Brandes H, Ulber B, Becker H, Vidal S. Evaluation of nine genotypes of oilseed rape (Brassica napus L.) for larval infestation and performance of rape stem weevil (Ceutorhynchus napi Gyll.). PLoS ONE. 2017;12:e0180807 pubmed publisher..napi is based on both antixenotic and antibiotic properties of the genotypes. The resynthesized line S30 should therefore be introduced into B. napus breeding programs to enhance resistance against C. napi. ..
- Hayes B, Panozzo J, Walker C, Choy A, Kant S, Wong D, et al. Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes. Theor Appl Genet. 2017;130:2505-2519 pubmed publisher..Using NIR and NMR predictions of quality traits overcomes a major barrier for the application of genomic selection for grain end-use quality traits in wheat breeding. ..
- Fang L, Wang Q, Hu Y, Jia Y, Chen J, Liu B, et al. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat Genet. 2017;49:1089-1098 pubmed publisher..Our results provide a genomic basis for improving cotton cultivars and for further evolutionary analysis of polyploid crops. ..
- Ohyama A, Shirasawa K, Matsunaga H, Negoro S, Miyatake K, Yamaguchi H, et al. Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato. Theor Appl Genet. 2017;130:1601-1616 pubmed publisher..As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study. ..
- Rincent R, Kuhn E, Monod H, Oury F, Rousset M, Allard V, et al. Optimization of multi-environment trials for genomic selection based on crop models. Theor Appl Genet. 2017;130:1735-1752 pubmed publisher..OptiMET is thus a valuable tool to determine optimal experimental conditions to best exploit MET and the phenotyping tools that are currently developed. ..
- Cabral D, Nunes J, Cabral P, Zuchi J, Raizer A, De Paula T. Implications of the clone by harvest interaction in the selection of sugarcane genotypes in a regionalized program. Genet Mol Res. 2017;16: pubmed publisher..In general, the grouping of the environments was inconsistent throughout the harvests, except for the E1 and E4 environments, which exhibited similarities for the different genotypes. ..
- Kwong Q, Teh C, Ong A, Chew F, Mayes S, Kulaveerasingam H, et al. Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.). BMC Genet. 2017;18:107 pubmed publisher..Machine learning slightly outperformed other methods, but required parameters optimization for GS implementation. ..
- Klápště J, Suontama M, Telfer E, Graham N, Low C, Stovold T, et al. Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens. PLoS ONE. 2017;12:e0185137 pubmed publisher..It therefore appeared that greater genetic variance may be due, at least in part, to contributions from inbreeding in these studied populations rather than a removal of inbreeding as is traditionally thought...
- Choi S, Yu X, Dhandapani V, Li X, Wang Z, Lee S, et al. Integrated analysis of leaf morphological and color traits in different populations of Chinese cabbage (Brassica rapa ssp. pekinensis). Theor Appl Genet. 2017;130:1617-1634 pubmed publisher..These robust QTLs and their candidate genes provide useful information for further research into leaf architecture with crop breeding. ..
- He J, Shao G, Wei X, Huang F, Sheng Z, Tang S, et al. Fine mapping and candidate gene analysis of qTAC8, a major quantitative trait locus controlling tiller angle in rice (Oryza sativa L.). PLoS ONE. 2017;12:e0178177 pubmed publisher..Our results provide a foundation for the cloning of qTAC8 and genetic improvement of the rice plant architecture. ..
- Pan C, Li Q, Lu Y, Zhang J, Yang X, Li X, et al. Chromosomal localization of genes conferring desirable agronomic traits from Agropyron cristatum chromosome 1P. PLoS ONE. 2017;12:e0175265 pubmed publisher..Therefore, the novel 1P addition and substitution lines will be used as important genetic materials to widen the genetic resources of wheat...
- Curtolo M, Cristofani Yaly M, Gazaffi R, Takita M, Figueira A, Machado M. QTL mapping for fruit quality in Citrus using DArTseq markers. BMC Genomics. 2017;18:289 pubmed publisher..sinensis and the identification of genes that may be responsible for phenotypic traits in Citrus. The obtained linkage map was used to assign sequences that had not been previously assigned to a position in the reference genome. ..
- Fu G, Wang G, Dai X. An adaptive threshold determination method of feature screening for genomic selection. BMC Bioinformatics. 2017;18:212 pubmed publisher..BE-IDC accommodates both the prediction accuracy and the computational speed that are highly demanded in the genomic selection. ..
- Hipparagi Y, Singh R, Choudhury D, Gupta V. Genetic diversity and population structure analysis of Kala bhat (Glycine max (L.) Merrill) genotypes using SSR markers. Hereditas. 2017;154:9 pubmed publisher..Therefore, Kala bhat genotypes can be a good source for the soybean breeding programme due to its better genetic diversity as well as its medicinal properties. ..
- Brzostowski L, Pruski T, Specht J, Diers B. Impact of seed protein alleles from three soybean sources on seed composition and agronomic traits. Theor Appl Genet. 2017;130:2315-2326 pubmed publisher..These results not only demonstrate the difficulty in developing cultivars with increased protein and yield but also provide information for breeding programs seeking to improve seed composition and agronomic traits simultaneously. ..
- Dong L, Liu S, Xu P, Deng W, Li X, Tharreau D, et al. Fine mapping of Pi57(t) conferring broad spectrum resistance against Magnaporthe oryzae in introgression line IL-E1454 derived from Oryza longistaminata. PLoS ONE. 2017;12:e0186201 pubmed publisher..Six candidate resistance genes were predicted in the target region according to the reference sequence of Nipponbare. These results could facilitate both marker-assisted selection for disease-resistant breeding and gene cloning...
- Bevan M, Uauy C, Wulff B, Zhou J, Krasileva K, Clark M. Genomic innovation for crop improvement. Nature. 2017;543:346-354 pubmed publisher..In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. ..
- Tan C, Cui C, Xiang Y, Ge X, Li Z. Development of Brassica oleracea-nigra monosomic alien addition lines: genotypic, cytological and morphological analyses. Theor Appl Genet. 2017;130:2491-2504 pubmed publisher..The B1, B4 and B5 chromosomes were transmitted by female at much higher rates (22.38-30.00%) than the other four (B3, B6, B7, B8) (5.04-8.42%). The MAALs should be valuable for exploiting the genome structure and evolution of B. nigra. ..
- Laidig F, Piepho H, Rentel D, Drobek T, Meyer U. Breeding progress, genotypic and environmental variation and correlation of quality traits in malting barley in German official variety trials between 1983 and 2015. Theor Appl Genet. 2017;130:2411-2429 pubmed publisher..Considerable yield progress and improvement of malting quality were achieved despite of their weak to moderate negative genetic dependence. ..
- Jena K, Hechanova S, Verdeprado H, Prahalada G, Kim S. Development of 25 near-isogenic lines (NILs) with ten BPH resistance genes in rice (Oryza sativa L.): production, resistance spectrum, and molecular analysis. Theor Appl Genet. 2017;130:2345-2360 pubmed publisher..These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries. ..
- Tränkner C, Pfeiffer N, Kirchhoff M, Kopisch Obuch F, van Dijk H, Schilhabel M, et al. Deciphering the complex nature of bolting time regulation in Beta vulgaris. Theor Appl Genet. 2017;130:1649-1667 pubmed publisher..Unexpectedly, one population segregated also for dwarf growth that was found to be controlled by a single locus on chromosome 9. ..
- Pacheco R, Duarte J, Branquinho R, Souza P. Environmental stratifications for soybean cultivar recommendation and its consistency over time. Genet Mol Res. 2017;16: pubmed publisher..The use of different genotypic sets across years reinforces the predictive value of the environmental stratification established. ..
- Rodrigues E, Daher R, Dos Santos A, Vivas M, Machado J, Gravina G, et al. Selecting elephant grass families and progenies to produce bioenergy through mixed models (REML/BLUP). Genet Mol Res. 2017;16: pubmed publisher..The individual 5 in the family Cana D'África x Guaçu/I.Z.2, planted in blocks 1 and 2, showed the highest dry biomass production. ..
- Cheng R, Kong Z, Zhang L, Xie Q, Jia H, Yu D, et al. Mapping QTLs controlling kernel dimensions in a wheat inter-varietal RIL mapping population. Theor Appl Genet. 2017;130:1405-1414 pubmed publisher..Mapping and marker identification of the kernel dimension-related QTLs definitely help realize the breeding goals. ..
- Sanchez C, Teodoro P, Londono S, Silva L, Peixoto L, Bhering L. Minimum number of measurements for evaluating soursop (Annona muricata L.) yield. Genet Mol Res. 2017;16: pubmed publisher..Our results indicate that selection of soursop genotypes with high fruit yield can be performed based on the third and fourth measurements in the early years and/or based on the eighth and ninth measurements at more advanced stages. ..
- Liu G, Zhao Y, Mirdita V, Reif J. Efficient strategies to assess yield stability in winter wheat. Theor Appl Genet. 2017;130:1587-1599 pubmed publisher..The huge potential of the developed strategy to select contrasting and informative environments has to be validated as a next step in an a priori scenario based on genotype-by-location interaction effects. ..
- Picard C, Gehring M. Proximal methylation features associated with nonrandom changes in gene body methylation. Genome Biol. 2017;18:73 pubmed publisher..These results provide new insights into the features determining the inheritance of gene body methylation and demonstrate that two different methylation equilibria can be maintained within single individuals. ..
- de Paula A, Dinato N, Vigna B, Fávero A. Recombinants from the crosses between amphidiploid and cultivated peanut (Arachis hypogaea) for pest-resistance breeding programs. PLoS ONE. 2017;12:e0175940 pubmed publisher..The hybrids between A. hypogaea and An 13 will be used in breeding programs seeking pest resistance, being subjected to successive backcrosses until recovering all traits of interest of A. hypogaea, keeping the pest resistance. ..
- Li Y, Tong L, Deng L, Liu Q, Xing Y, Wang C, et al. Evaluation of ZmCCT haplotypes for genetic improvement of maize hybrids. Theor Appl Genet. 2017;130:2587-2600 pubmed publisher..Of nine resistant ZmCCT haplotypes, haplotype H5 exhibited excellent performance for both flowering time and stalk rot resistance and is thus expected to have potential value in future maize breeding programs. ..
- Marini N, Bevilacqua C, Büttow M, Raseira M, Bonow S. Identification of reference genes for RT-qPCR analysis in peach genotypes with contrasting chilling requirements. Genet Mol Res. 2017;16: pubmed publisher..This study is the first survey of the stability of reference genes in peaches under chilling stress and provides guidelines for more accurate RT-qPCR results. ..
- Crespo Herrera L, Garkava Gustavsson L, Ahman I. A systematic review of rye (Secale cereale L.) as a source of resistance to pathogens and pests in wheat (Triticum aestivum L.). Hereditas. 2017;154:14 pubmed publisher..the current human population growth rate, there is an increasing need to raise wheat productivity by means of plant breeding, along with development of more efficient and sustainable agricultural systems...
- Dalmais M, Antelme S, Ho Yue Kuang S, Wang Y, Darracq O, d Yvoire M, et al. A TILLING Platform for Functional Genomics in Brachypodium distachyon. PLoS ONE. 2013;8:e65503 pubmed publisher..The mutant population and the TILLING platform should greatly facilitate functional genomics approaches in this model organism. ..