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Factors affecting genomic selection revealed by empirical evidence in maize

The Crop Journal 2018年第4期6卷 341-352页

作者： Xiaogang Liu Hongwu Wang Hui Wang Zifeng Guo Xiaojie Xu Jiacheng Liu Shanhong Wang Wen-Xue Li Cheng Zou Boddupalli M.Prasanna Michael S.Olsen Changling Huang Yunbi Xu Institute of Crop Science National Key Facility of Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural Sciences international maize and wheat improvement center (cimmyt) ICRAF campus international maize and wheat improvement center (cimmyt)

Genomic selection(GS) as a promising molecular breeding strategy has been widely implemented and evaluated for plant breeding, because it has remarkable superiority in enhancing genetic gain, reducing breeding time and expenditure, and accelerating the breeding process. In this study the factors affecting prediction accuracy(rMG) in GS were evaluated systematically, using six agronomic traits(plant height, ear height, ear length, ear diameter,grain yield per plant and hundred-kernel weight) evaluated in one natural and two biparental populations. The factors examined included marker density, population size, heritability,statistical model, population relationships and the ratio of population size between the training and testing sets, the last being revealed by resampling individuals in different proportions from a population. Prediction accuracy continuously increased as marker density and population size increased and was positively correlated with heritability; rMGshowed a slight gain when the training set increased to three times as large as the testing set. Low predictive performance between unrelated populations could be attributed to different allele frequencies, and predictive ability and prediction accuracy could be improved by including more related lines in the training population. Among the seven statistical models examined, including ridge regression best linear unbiased prediction(RR-BLUP), genomic BLUP(GBLUP), Bayes A, Bayes B, Bayes C, Bayesian least absolute shrinkage and selection operator(Bayesian LASSO), and reproducing kernel Hilbert space(RKHS), the RKHS and additive-dominance model(Add + Dom model) showed credible ability for capturing non-additive effects, particularly for complex traits with low heritability. Empirical evidence generated in this study for GS-relevant factors will help plant breeders to develop GS-assisted breeding strategies for more efficient development of varieties.

关键词： Marker density Population size Population relationship Zea mays

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Genetic improvement of wheat grain quality at cimmyt

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Frontiers of Agricultural Science and Engineering 2019年第3期6卷 265-272页

作者： Carlos GUZMáN Karim AMMAR Velu GOVINDAN Ravi SINGH Global wheat Program The International Maize and Wheat Improvement Center (CIMMYT)

The international maize and wheat improvement center(cimmyt) is the global leader in publiclyfunded maize and wheat research and in farming systems based on these *** leads the Global wheat Program(GWP), which includes some of the largest wheat breeding programs in the *** GWP has been successful in developing wheat germplasm that is used extensively *** quality improvement is a central component of all the breeding efforts at cimmyt and the wheat Chemistry and Quality Laboratory represents an integral part of the breeding *** quality is addressed at cimmyt over the full range of this very wide and variable concept with milling,processing, end-use and nutritional quality *** progenitors and advanced lines developed by the breeders are assessed for diverse quality attributes, with the aim of identifying those that fulfill the requirements in terms of milling, processing, end-use and nutritional quality in different target *** research is conducted to make more efficient the integration of wheat quality traits in the breeding *** main topics being addressed are(1) methodologies to analyze grain quality traits,(2) genetic control and environmental effects on quality traits,(3) characterization of genetic resources for quality improvement, and(4) diversifying grain properties for novel uses.

关键词： biofortification breeding grain quality wheat

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Dissecting maize Productivity:Ideotypes Associated with Grain Yield under Drought Stress and Well-watered Conditions

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Journal of Integrative Plant Biology 2012年第12期54卷 1007-1020页

作者： Jill E.Cairns Ciro Sanchez Mateo Vargas Raziel Ordoez Jose Luis Araus Global maize Program International Maize and Wheat Improvement Center(CIMMYT)Mexico D.F.Mexico Bioinformatics and Statistics Unit International Maize and Wheat Improvement Center(CIMMYT)Mexico D.F.Mexico Unit of Plant Physiology Department of Plant BiologyUniversity of BarcelonaBarcelonaSpain

To increase maize （Zea mays L.） yields in drought-prone environments and offset predicted maize yield losses under future climates, the development of improved breeding pipelines using a multi-disciplinary approach is essential. Elucidating key growth processes will provide opportunities to improve drought breeding progress through the identification of key phenotypic traits, ideotypes, and donors. In this study, we tested a large set of tropical and subtropical maize inbreds and single cross hybrids under reproductive stage drought stress and well-watered conditions. Patterns of biomass production, senescence, and plant water status were measured throughout the crop cycle. Under drought stress, early biomass production prior to anthesis was important for inbred yield, while delayed senescence was important for hybrid yield. Under well-watered conditions, the ability to maintain a high biomass throughout the growing cycle was crucial for inbred yield, while a stay-green pattern was important for hybrid yield. While new quantitative phenotyping tools such as spectral reflectance （Normalized Difference Vegetation Index, NDVI） allowed for the characterization of growth and senescence patterns as well as yield, qualitative measurements of canopy senescence were also found to be associated with grain yield.

关键词： Climate change drought stress ideotypes maize senescence spectral reflectance.

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Phenotyping for Abiotic Stress Tolerance in maize

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Journal of Integrative Plant Biology 2012年第4期54卷 238-249页

作者： Benhilda Masuka Jose Luis Araus Biswanath Das Kai Sonder Jill E.Cairns international maize and wheat improvement center(cimmyt) Unit of Plant Physiology Faculty of BiologyUniversity of Barcelona cimmyt Km 45 Carretera Mexico-Veracruz

The ability to quickly develop germplasm having tolerance to several complex polygenic inherited abiotic and biotic stresses combined is critical to the resilience of cropping systems in the face of climate change. Molecular breeding offers the tools to accelerate cereal breeding; however, suitable phenotyping proto- cols are essential to ensure that the much-anticipated benefits of molecular breeding can be realized. To facilitate the full potential of molecular tools, greater emphasis needs to be given to reducing the within-experimental site variability, application of stress and characterization of the environment and appropriate phenotyping tools. Yield is a function of many processes throughout the plantcycle, and thus integrative traits that encompass crop performance over time or organization level （i.e. canopy level） will provide a better alternative to instantaneous measurements which provide only a snapshot of a given plant process. Many new phenotyping tools based on remote sensing are now available including non-destructive measurements of growth-related parameters based on spectral reflectance and infrared thermometry to estimate plant water status. Here we describe key field phenotyping protocols for maize with emphasis on tolerance to drought and low nitrogen.

关键词： Drought low nitrogen tolerance maize phenotyping spatial variability.

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Sustainable intensification of African agriculture:a necessity,but not yet a reality

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Frontiers of Agricultural Science and Engineering 2020年第4期7卷 383-389页

作者： Bruno GÉRARD international maize and wheat improvement center(cimmyt) Texcoco 56237Mexico

After decades of well-intentioned and professional research for development,agriculture in sub-Saharan Africa is still dominated by low-input,subsistence food crop production on small,rainfed land holdings using hand *** are the drivers and constraints to development in African agriculture,and how can the region intensify farming in economical and environmentally sustainable ways to satisfy its rapidly rising and shifting food demands?

关键词： Sustainable agriculture shifting

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Redesigning crop varieties to win the race between climate change and food security

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Molecular Plant 2023年第10期16卷 1590-1611页

作者： Kevin V.Pixley Jill E.Cairns Santiago Lopez-Ridaura Chris O.Ojiewo Maryam Abba Dawud Inoussa Drabo Taye Mindaye Baloua Nebie Godfrey Asea Biswanath Das Happy Daudi Haile Desmae Benoit Joseph Batieno Ousmane Boukar Clare T.M.Mukankusi Stanley T.Nkalubo Sarah J.Hearne Kanwarpal S.Dhugga Harish Gandhi Sieglinde Snapp Ernesto Adair Zepeda-Villarreal international maize and wheat improvement center(cimmyt) TexcocoMexico international maize and wheat improvement center(cimmyt) HarareZimbabwe international maize and wheat improvement center(cimmyt) NairobiKenya Lake Chad Research Institute(LCRI) MaidiguriNigeria international maize and wheat improvement center(cimmyt) DakarSenegal Ethiopian Institute of Agricultural Research(EIAR) Addis AbabaEthiopia National Agricultural Research Organization(NARO) KampalaUganda Tanzania Agricultural Research Institute(TARI) NaliendeleTanzania Institut de l'Environnement et de Recherches Agricoles(INERA) OuagadougouBurkina Faso international Institute of Tropicl Agriculture(IITA) KanoNigeria Alliance of Bioversity international and CIAT KampalaUganda

Climate change poses daunting challenges to agricultural production and food *** temperatures,shifting weather patterns,and more frequent extreme events have already demonstrated their effects on local,regional,and global agricultural *** varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance,productivity,and profitability under climate-changed *** surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet,sorghum,maize,groundnut,cowpea,and common bean varieties,particularly in sub-Saharan *** then review the current progress and prospects for breeding three prioritized future-essential traits for each of these *** predict that most current breeding priorities will remain important,but that rates of genetic gain must increase to keep pace with climate challenges and consumer ***,the predicted future-essential traits include innovative breeding targets that must also be prioritized;for example,(1)optimized rhizosphere microbiome,with benefits for P,N,and water use efficiency,(2)optimized performance across or in specific cropping systems,(3)lower nighttime respiration,(4)improved stover quality,and(5)increased early *** further discuss cutting-edge tools and approaches to discover,validate,and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision,accuracy,and *** conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.

关键词： climate change food security crop breeding cropping systems expert survey sub-Saharan Africa

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Identification and validation of stable quantitative trait loci for yield component traits in wheat

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The Crop Journal 2023年第2期11卷 558-563页

作者： Lingli Li Yingjie Bian Yan Dong Jie Song Dan Liu Jianqi Zeng Fengju Wang Yong Zhang Zhonghu He Xianchun Xia Yan Zhang Shuanghe Cao Institute of Crop Sciences National Wheat Improvement CenterChinese Academy of Agricultural SciencesBeijing 100081China international maize and wheat improvement center(cimmyt)China Office Beijing 100081China

Grain weight and grain number are important yield component traits in wheat and identification of underlying genetic loci is helpful for improving ***,we identified eight stable quantitative trait loci(QTL)for yield component traits,including five loci for thousand grain weight(TGW)and three for grain number per spike(GNS)in a recombinant inbred line population derived from cross Yangxiaomai/Zhongyou 9507 across four *** grain size is a major determinant of grain weight,we also mapped QTL for grain length(GL)and grain width(GW).***-2D,***-3B,***-5A and ***-7A.2 for TGW co-located with those for grain ***-2D also had a consistent genetic position with ***-2D,suggesting that the pleiotropic locus is a modulator of trade-off effect between TGW and *** and linkage mapping showed that TaGL3-5A and WAPO-A1 were candidate genes of ***-5A and ***-7A.2,*** developed Kompetitive allele specific PCR(KASP)markers linked with the stable QTL for yield component traits and validated their genetic effects in a diverse panel of wheat cultivars from the Huang-Huai River Valley ***-based genotyping analysis further revealed that the superior alleles of all stable QTL for TGW but not GNS were subject to positive selection,indicating that yield improvement in the region largely depends on increased *** analyses with previous studies showed that most of the QTL could be detected in different genetic backgrounds,and ***-7A.1 is likely a new *** findings provide not only valuable genetic information for yield improvement but also useful tools for marker-assisted selection.

关键词： Grain number per spike KASP marker QTL mapping Thousand grain weight Triticum aestivum

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A SSR Linkage Map of maizex Teosinte F_2 Population and Analysis of Segregation Distortion

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Agricultural Sciences in China 2011年第2期10卷 166-174页

作者： ZHOU Jun-qing GUO Yu-qiu GAO Yu-feng LI Jian-sheng YAN Jian-bing National maize improvement center of China China Agricultural UniversityBeijing 00P.R.China international maize and wheat improvement center（cimmyt） Mexico D.F.06600Mexico

In this study,a linkage genetic map was constructed using a F2 population derived from a cross between a elite maize inbred,B73,and its progenitor,Teosinte（*** ***）,through 205 simple sequence repeat（SSR） markers and one morphological *** Mapmaker 3.0,polymorphic markers were clustered into 10 groups,covering 10 chromosomes of maizexteosinte,with a total length of 2 002.4 cM and an average interval of 9.7 *** errors were detected using R/QTL（LOD=2.0） in 109 markers referring to 176 individuals,distributed across all 10 chromosomes with a ratio 1.2%.Projected error loci were re-run and 304 out of the 460 were confirmed as errors and replaced.A new linkage map was constructed,in which markers maintained the same order but the total map length decreased to 1 947.8 cM,with an average interval of 9.4 cM between *** total,25.2%（P0.05） markers were identified to have segregation distortion,in which 34.6% deviated towards the pollination parent（B73）,30.8% deviated towards Teosinte,32.7% deviated towards heterozygote and 1.9% deviated towards both *** map was also compared with published maizexteosinte and maize IBM map.

关键词： maize molecular linkage map segregation distortion simple sequence repeat teosinte

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Characterization of TaCOMT genes associated with stem lignin content in common wheat and development of a gene-specific marker

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Journal of Integrative Agriculture 2019年第5期18卷 939-947页

作者： FU Lu-ping XIAO Yong-gui YAN Jun LIU Jin-dong WEN Wei-e ZHANG Yong XIA Xian-chun HE Zhong-hu National wheat improvement center/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Institute of Cotton Research Chinese Academy of Agricultural Sciences international maize and wheat improvement center (cimmyt) China Office

Stem lignin content(SLC) in common wheat(Triticum aestivum L.) contributes to lodging resistance. Caffeic acid 3-O-methyltransferase(COMT) is a key enzyme involved in lignin biosynthesis. Characterization of TaCOMT genes and development of gene-specific markers could enable marker-assisted selection in wheat breeding. In the present study, the full-length genomic DNA(gDNA) sequences of TaCOMT genes located on chromosomes 3 A, 3 B, and 3 D were cloned by homologous cloning. Two allelic variants, TaCOMT-3 Ba and TaCOMT-3 Bb, were identified and differed by a 222-bp insertion/deletion(InDel) in the 3′-untranslated region(3′-UTR). A co-dominant gene-specific marker based on this InDel was developed and designated as Ta COMT-3 BM. A total of 157 wheat cultivars and advanced lines grown in four environments were used to validate the associations between allelic patterns and SLC. The SLC of cultivars with TaCOMT-3 Ba was significantly(Pwheat breeding.

关键词： Triticum aestivum L. caffeic acid 3-O-methyltransferase stem lignin content gene-specific marker lodging resistance

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Changes in soil biochemical indicators at different wheat growth stages under conservation-based sustainable intensification of rice-wheat system

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Journal of Integrative Agriculture 2018年第8期17卷 1871-1880页

作者： Tanushree Bera Sandeep Sharma H.S.Thind Yadvinder-Singh H.S.Sidhu M.L.Jat Department of Soil Science Punjab Agricultural University Borlaug Institute for South Asia (BISA) International Maize and Wheat Improvement Center (CIMMYT) cimmyt National Agricultural Science Complex

Soil microbes play critical roles in soil biogeochemistry, soil biological health and crop productivity. The current study evaluated the effects of tillage and residue management on changes in soil biochemical indicators at different growth stages of wheat after 5 years of rice-wheat system. Nine treatment combinations of tillage, crop establishment and crop residue management included three main plot treatments applied to rice:(1) conventional till direct dry seeded rice(CTDSR),(2) zero till direct dry seeded rice(ZTDSR), and(3) conventional puddled manual transplanted rice(CTPTR) and three subplot treatments in subsequent wheat:(1) conventional tillage with rice residue removed(CTW-R),(2) zero tillage with rice residue removed(ZTW-R) and(3) zero tillage with rice residue retained as surface mulch(ZTW+R). Irrespective of rice treatments, ZTW+R treatment had higher soil biochemical indicators compared with ZTW-R and CTW-R at all the growth stages of wheat. Generally, all the biochemical indicators were the highest at the flowering stage of wheat. Residual effect of rice treatments was also significant on biochemical quotients in wheat, which were the highest under ZTDSR followed by CTDSR and CTPTR. The present study provided three sensitive and reliable biochemical indicators(microbial biomass, basal soil respiration and microbial quotient) which respond rapidly to change in tillage and residue management practices in RWS of South Asia.

关键词： microbial metabolic quotients tillage practices residue retention cropping system

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