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The role of genomic structural variation in the genetic improvement of polyploid crops

The Crop Journal 2019年第2期7卷 127-140页

作者： Sarah-Veronica Schiessl Elvis Katche Elizabeth Ihien Harmeet Singh Chawla Annaliese S.Mason department of plant breeding Justus Liebig University

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.

关键词： Presence–absence variation Copy-number variation Homeologous exchanges Genome structure Pan-genome

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SRG1,Encoding a Kinesin-4 Protein,Is an Important Factor for Determining Grain Shape in Rice

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Rice science 2018年第6期25卷 297-307页

作者： QIN Ran Delara AKHTER YANG Chengcong Ujjal Kumar NATH Jamal ESHAG JIN Xiaoli SHI Chunhai department of Agronomy Zhejiang University department of Genetics and plant breeding Sylhet Agricultural University department of Genetics and plant breeding Bangladesh Agricultural University

Grain shape is one of the important agronomic traits, which is closely related to the yield of rice.A new rice mutant, named small and round grain(srg1), was isolated from an indica cultivar Zhenong 34 by ethyl methane sulfonate(EMS) mutagenesis. The microscopic analysis showed that the cell length of spikelet in srg1 was decreased compared with that in wild type(WT), which caused the grain length ***, the grains of srg1 were wider than those of WT because of the increased cell layers in spikelet in the lateral direction. Therefore, the inhibition of cell expansion and increased cell proliferation collectively led to the small and round grain. By map-based cloning, the gene SRG1 was located on the short arm of chromosome 9, which encodes a kinesin-4 protein, represented by the gene LOC_Os09 g02650. A single nucleotide polymorphism, occurred in the 16 th exon of SRG1, led to premature translation stop in mutant. The cell cycle-related genes were up-regulated in srg1, which conferred that SRG1 controlled grain width through the cell proliferation. Since the role of SRG1 in regulating grain shape was not clarified well before, it is valuable to explore the mechanism of grain development. This study could, hence, provide a morphogenesis and molecular basis for elucidating the function of SRG1, as well as a new germplasm resource for the further study of grain development.

关键词： small and round grain kinesin-4 protein gene mapping rice

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Microbial starch-binding domains are superior to granule-bound starch synthase I for anchoring luciferase to potato starch granules

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Progress in Natural Science:Materials International 2006年第12期16卷 1295-1299页

作者： Jean-Paul VINCKEN Luc C.J.M. SUURS Richard G.F. VISSER Laboratory of plant breeding Department of Plant Sciences Wageningen University Wageningen The Netherlands

Microbial starch-binding domains (SBD) and granule-bound starch synthase I (GBSSI) are proteins which are accumulated in potato starch granules. The efficiency of SBD and GBSSI for targeting active luciferase reporter proteins to granules during starch biosynthesis was compared. GBSSI or SBD sequences were fused to the N- or C-terminus of the luciferase (LUC) gene, via an artificial Pro-Thr encoding linker sequence. The genes were introduced into an amylose-free (amf) potato mutant. It appeared that SBD was superior to GBSSI as a targeting sequence, mainly because the luciferase retained higher activity in the SBD-containing fusion proteins than in the GBSSI-containing ones.

关键词： luciferase GBSS I SBD amf potato.

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Genetic and Genotype × Environment Interaction Effects for Appearance Quality of Rice

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Agricultural Sciences in China 2009年第8期8卷 891-901页

作者： Sharifi Peyman Dehghani Hamid Mumeni Ali Moghaddam Mohammad department of plant breeding Faculty of Agriculture Tarbiat Modares University Rice Research Institute of Iran (RRII) department of Agronomy and plant breeding Faculty of Agriculture Tabriz University

This study was conducted to generate genetic information in rice varieties based on a complete diallel crosses over two years. The results indicated that genotype effect was significant for all traits. Genotype × environment interaction effects were significant only for cooked grain length （CGL） and cooked grain shape （CGSH）. General combining ability （GCA） and specific combining ability （SCA） effects were significant for entire traits, which indicated the important roles of both additive and non-additive gene actions. GCA x environment interaction effects were significant for CGL, CGSH and grain elongation index （GEI）. In the controlling of the inheritance of milled grain shape （GSH）, milled grain width （MGW）, GEI, milled grain length （MGL）, CGSH and cooked grain width （CGW）, the additive gene effects were more important than non-additive one. The average degree of dominance was within the range of partial dominance for all of the traits. The narrow-sense heritability was ranged from 0.65 （GSH） to 0.36 （CGL）. GCA effects were significant for all of the parents in milled grain length and it was significant for some of the parents in other traits. The crosses of Deilmani × IRFAON-215 exhibited significant SCA for GEI. The positive mean of heterosis was observed for CGW. The highest maximum values of heterosis were revealed in GEI, flowed by GSH, MGW and CGW. GCA and MPV were significantly and positively correlated together for all traits.

关键词： appearance quality diallel analysis genetic main effects environment interaction milling quality rice

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Responses of Four Rice Varieties to Elevated CO_2 and Different Salinity Levels

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Rice science 2018年第3期25卷 142-151页

作者： Sheidollah KAZEMI Hamid Reza ESHGHIZADEH Morteza ZAHEDI department of Agronomy and plant breeding College of Agriculture Isfahan University of Technology

This study was carried out in 2014 at Isfahan University of Technology, Iran, to evaluate the responses of four rice varieties(Neda, Deylamani, Shiroudi and Domsorkh) to ambient(360 ± 50 μmol/mol) and elevated(700 ± 50 μmol/mol) air carbon dioxide(CO_2) concentrations under four salinity levels(0, 30, 60 and 90 mmol/L Na Cl). There was significant variation among rice varieties in response to elevated CO_2 concentration under the four salinity levels. Under non-saline condition, elevated CO_2 increased the dry weight of Neda, Deylamani and Domsorkh by 8%, 50% and 8%, respectively, but reversely decreased that of Shiroudi by 34%. Increasing CO_2 concentration significantly reduced the negative effects of salinity on Shiroudi, but these effects were even increased in Deylamani and Domsorkh under all the salinity levels and in Neda only under 30 and 60 mmol/L Na Cl. Significant correlations were established between plant dry weight, SPAD value and leaf area under both CO_2 levels. However, this trend was observed only at ambient CO_2 concentration in the presence of soluble carbohydrates. The results revealed the genotype and salinity dependence of the effects of CO_2 concentrations on the rice traits investigated.

关键词： CO2 concentration genetic diversity salt tolerance water soluble carbohydrate

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Partial Relief of Drought-Stressed Fennel(Foeniculum vulgare Mill.) in Response to Foliar-Applied Zinc

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Pedosphere 2019年第6期29卷 752-763页

作者： Ahmad RAJABI Parviz EHSANZADEH Jamshid RAZMJOO department of Agronomy and plant breeding College of Agriculture Isfahan University of Technology

Few attempts have been made to explore the effect of Zn fertilization on the performance of medicinal plants in general and fennel in particular, under adverse conditions. This study was conducted to examine the efficacy of zinc (Zn) in correcting physiological responses of fennel to water deficit. Twelve field-grown fennel genotypes were subjected to two levels of irrigation (irrigation after 25%–35% and 75%–85% depletion of available soil water) and two levels of foliar-applied Zn (0 and 4 g kg −1 ). Water deprivation had significant effects on all characteristics;i.e., in contrast to seed essential oil concentration, harvest index, and superoxide dismutase (SOD) and catalase activities, it led to decreases in the rest of the attributes. Varietal differences in response to drought were meaningful for most of the traits. Genotypic variations for dry mass and seed yield were consistent with differences among the genotypes in leaf water potential, relative water content, proline concentration, and chlorophyll concentrations. Zinc led to significant increases in all physiological attributes, including activation of antioxidant defense responses manifested in ascorbate peroxidase and SOD activities and carotenoid concentration. The Zn-effect tended to be more notable in drought-stricken fennel plants in a majority of the traits. Based on our findings, Zn could be considered an effective micronutrient for ameliorating, at least in part, the stressful effects of water deficit on fennel.

关键词： Antioxidant defense Drought tolerance Medicinal plant Micronutrient Physilogical attributes Water deficit Zn fertilization

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Effects of Salinity and Potassium Application on Antioxidant Enzyme Activities and Physiological Parameters in Pearl Millet

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Agricultural Sciences in China 2011年第2期10卷 228-237页

作者： Mostafa Heidari Parisa Jamshidi Faculty of Agronomy and plant breeding department University of Zabol department of Agronomy University of Zabol

A plot culture experiment was conducted in a greenhouse at University of Zabol,Iran,to study the effects of different salinity levels and potassium supply on pearl *** experiment was laid out in a completely randomized factorial design with three *** sulfate was used as the potassium *** rates of potassium treatments were 0,100,and 200 kg *** millet was subjected to different salinity levels（0,4,8,and 12 ds m-1） through addition of NaCl to irrigation *** showed that the increase in the salt concentration from control to 12 ds m-1 decreased grain yield（38.7%） of millet *** this study,we found a negative relationship between potassium and proline accumulation at vegetative（r2=-0.75＊＊） and reproductive stage（r2=-0.66＊＊） in millet *** stress remarkably elevated the activities of CAT and GPX antioxidant enzymes at vegetative and reproductive ***,potassium application had significant effect on grain yield and increased it about 10.6% at the highest salinity treatment（12 ds m-1）.Though,potassium treatment increased antioxidant activity in millet plants,it had no significant effect on proline content in *** treatment decreased potassium uptake but application potassium increased potassium content in leaves at two stages.

关键词： antioxidants enzymes ion content pearl millet potassium proline salinity

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Proteomic Profiling and Protein-Protein Interaction Network Reveal the Molecular Mechanisms of Susceptibility to Drought Stress in Canola(Brassica napus L.)

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Phyton-International Journal of Experimental Botany 2022年第7期91卷 1403-1417页

作者： Reza Shokri-Gharelo Ali Bandehagh Mohammad Anwar Hossain department of plant breeding and Biotechnology University of TabrizTabriz51368Iran department of Genetics and plant breeding Bangladesh Agricultural UniversityMymensingh2202Bangladesh

Drought stress is one of the most important abiotic stresses that plants face frequently in *** drought conditions,many morphological,physiological,and molecular aspects of plants are changed and as a result plants experience a remarkable reduction in growth,yield,and *** expand our understanding of the molecular basis of the plant response to drought stress,the proteomic profile and protein-protein network of canola(Brassica napus L.)were *** focus was to show molecular mechanisms related to canola susceptibility to drought *** experiment used a completely randomized design,implemented in a hydroponic system under greenhouse *** impose drought stress,plants were exposed to Hoagland’s solution supplemented with polyethylene glycol(PEG)6000 for 7 *** drought stress resulted in 161reproducible protein spots in twodimensional electrophoresis of canola *** t-student test showed 21 differentially abundant proteins(DAP),of which 2 and 19 were up and down accumulated,*** spots identified as 1-aminocyclopropane-1-carboxylate oxidase and D-2-hydroxyglutarate dehydrogenase showed an increased abundance of 2.11 and 1.77,*** extended protein-protein interaction of differentially abundant proteins and KEGG analysis showed 47 pathways directly and indirectly associated with canola response to drought *** with increased abundance were associated with amino acid and signaling processes,whereas DAPs with decreased abundance were mostly connected with pathways responsible for energy *** results of the study will help to elucidate further the molecular events associated with the susceptibility to drought stress in canola.

关键词： Abiotic stress differentially abundant protein molecular function proteomics susceptibility

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Genetic diversity and population structure analysis of Pistacia species revealed by phenylalanine ammonia-lyase gene markers and implications for conservation

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Journal of Forestry Research 2018年第4期29卷 986-996页

作者： Setareh Mirzavand Karim Sorkheh Mohammad Reza Siahpoosh department of Agronomy and plant breeding Faculty of AgricultureShahid Chamran University of Ahvaz

Information on population genetic structure and crop genetic diversity is important for genetically improving crop species and conserving threatened species. The PAL gene sequence is part of a multigene family that can be utilized to design DNA marker systems for genetic diversity and population structure investigation. In the current study, genetic diversity and population structure of 100 accessions of wild Pistacia species were investigated with 78 PAL markers. A protocol for using PAL sequences as DNA markers was developed. A total of 313 PAL loci were recognized, showing 100% polymorphism for PAL markers. The PAL markers produced relatively more observed and effective alleles in Pistacia falcata and Pistacia atlantica, with a higher Shannon＇s information index and expected heterozygosity in P. atlantica, Pistacia vera and Pistacia mutica. Pairwise assessment of Nei＇s genetic distance and genetic identity between populations revealed a close association between geographically iso- lated populations of Pistacia khinjuk and Pistacia chinensis. The accessions of wild Pistacia species had more genetic relationship among studied groups of species. Analysis of molecular variance indicated 19% among- population variation and 81% within-population variation for the PAL gene based DNA marker. Population structure analysis based on PAL revealed four groups with high genetic admixture among populations. The results establish PAL markers as a functional DNA marker system and provide important genetic information about accessions from wild populations of Pistacia species.

关键词： Genetic relationship Classification Geneticresources PAL Phenylalanine ammonia-lyase gene

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Investigating seed mineral composition in Korean landrace maize(Zea mays L.) and its kernel texture specificity

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Journal of Integrative Agriculture 2019年第9期18卷 1996-2005页

作者： Sooyeon Lim Gibum Yi department of plant Science Plant Genomics and Breeding Institute/Research Institute of Agriculture and Life Sciences Seoul National University

Mineral malnutrition affects billions of people all over the world and biofortification of staple crops provides a potential way to alleviate dietary mineral *** example,nutritional quality is an important breeding target for fresh waxy maize(Zea mays L.),which is widely consumed in Asian *** improvement of mineral composition will require comprehensive profiling of the mineral composition of maize varieties and an understanding of the capacity for maize grains to accumulate ***,using inductively coupled plasma absorption emission spectrometry,we quantified 12 minerals from the seeds of 47 maize varieties,including 25 Korean *** also compared the mineral contents in varieties with different seed starch profiles:waxy maize(which contains 100%amylopectin),dent maize(roughly 75%amylopectin and 25%amylose),and flint maize(similar to dent maize).The amounts of potassium,phosphorus,and sulfur were correlated with seed texture,waxy maize having higher amounts of phosphorus and potassium than dent maize and lower amounts of sulfur than flint maize or dent *** addition,a positive relationship was detected between the amount of phosphorus and that of potassium,magnesium,and *** results provide information on maize seed mineral composition and indicate that it could be affected by starch ***,the landraces that exhibit high mineral contents could be used as germplasm materials for breeding programs aimed at producing biofortified maize cultivars.

关键词： micronutrient macronutrient biofortification maize aleurone endosperm

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