Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance

Abstract Background Drought threatens the food supply of the world population. Dissecting the dynamic responses of plants to drought will be beneficial for breeding drought-tolerant crops, as the genetic controls of these responses remain largely unknown. Results Here we develop a high-throughput multiple optical phenotyping system to noninvasively phenotype 368 maize genotypes with or without drought stress over a course of 98 days, and collected multiple optical images, including color camera scanning, hyperspectral imaging, and X-ray computed tomography images. We develop high-throughput analysis pipelines to extract image-based traits (i-traits). Of these i-traits, 10,080 were effective and heritable indicators of maize external and internal drought responses. An i-trait-based genome-wide association study reveals 4322 significant locus-trait associations, representing 1529 quantitative trait loci (QTLs) and 2318 candidate genes, many that co-localize with previously reported maize drought responsive QTLs. Expression QTL (eQTL) analysis uncovers many local and distant regulatory variants that control the expression of the candidate genes. We use genetic mutation analysis to validate two new genes, ZmcPGM2 and ZmFAB1A, which regulate i-traits and drought tolerance. Moreover, the value of the candidate genes as drought-tolerant genetic markers is revealed by genome selection analysis, and 15 i-traits are identified as potential markers for maize drought tolerance breeding. Conclusion Our study demonstrates that combining high-throughput multiple optical phenotyping and GWAS is a novel and effective approach to dissect the genetic architecture of complex traits and clone drought-tolerance associated genes.

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Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars

BMC Plant Biology ◽

10.1186/s12870-016-0777-5 ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 19

Author(s):

Luciana Souto Mofatto ◽

Fernanda de Araújo Carneiro ◽

Natalia Gomes Vieira ◽

Karoline Estefani Duarte ◽

Ramon Oliveira Vidal ◽

...

Keyword(s):

Drought Tolerance ◽

Candidate Genes ◽

High Throughput ◽

Shoot Apex ◽

Coffea Arabica ◽

High Throughput Sequencing

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Genomic basis underlying the metabolome-mediated drought adaptation of maize

Genome Biology ◽

10.1186/s13059-021-02481-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Fei Zhang ◽

Jinfeng Wu ◽

Nir Sade ◽

Si Wu ◽

Aiman Egbaria ◽

...

Keyword(s):

Environmental Stress ◽

Candidate Genes ◽

Genetic Control ◽

Stress Responses ◽

Complex Traits ◽

Inbred Lines ◽

Drought Response ◽

Eqtl Analysis ◽

Drought Adaptation ◽

Hub Genes

Abstract Background Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underlying crop environmental stress adaptation remains elusive. Results Here, we perform non-targeted metabolic profiling of leaves for 385 maize natural inbred lines grown under well-watered as well as drought-stressed conditions. A total of 3890 metabolites are identified and 1035 of these are differentially produced between well-watered and drought-stressed conditions, representing effective indicators of maize drought response and tolerance. Genetic dissections reveal the associations between these metabolites and thousands of single-nucleotide polymorphisms (SNPs), which represented 3415 metabolite quantitative trait loci (mQTLs) and 2589 candidate genes. 78.6% of mQTLs (2684/3415) are novel drought-responsive QTLs. The regulatory variants that control the expression of the candidate genes are revealed by expression QTL (eQTL) analysis of the transcriptomes of leaves from 197 maize natural inbred lines. Integrated metabolic and transcriptomic assays identify dozens of environment-specific hub genes and their gene-metabolite regulatory networks. Comprehensive genetic and molecular studies reveal the roles and mechanisms of two hub genes, Bx12 and ZmGLK44, in regulating maize metabolite biosynthesis and drought tolerance. Conclusion Our studies reveal the first population-level metabolomes in crop drought response and uncover the natural variations and genetic control of these metabolomes underlying crop drought adaptation, demonstrating that multi-omics is a powerful strategy to dissect the genetic mechanisms of crop complex traits.

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Unraveling the Genetic Architecture of Two Complex, Stomata-Related Drought-Responsive Traits by High-Throughput Physiological Phenotyping and GWAS in Cowpea (Vigna. Unguiculata L. Walp)

Frontiers in Genetics ◽

10.3389/fgene.2021.743758 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xinyi Wu ◽

Ting Sun ◽

Wenzhao Xu ◽

Yudong Sun ◽

Baogen Wang ◽

...

Keyword(s):

Drought Tolerance ◽

Genetic Mapping ◽

Soil Water ◽

Water Relations ◽

High Throughput ◽

Genetic Architecture ◽

Stomatal Closure ◽

Significant Snps ◽

Soil Drought ◽

Stomatal Control

Drought is one of the most devasting and frequent abiotic stresses in agriculture. While many morphological, biochemical and physiological indicators are being used to quantify plant drought responses, stomatal control, and hence the transpiration and photosynthesis regulation through it, is of particular importance in marking the plant capacity of balancing stress response and yield. Due to the difficulties in simultaneous, large-scale measurement of stomatal traits such as sensitivity and speed of stomatal closure under progressive soil drought, forward genetic mapping of these important behaviors has long been unavailable. The recent emerging phenomic technologies offer solutions to identify the water relations of whole plant and assay the stomatal regulation in a dynamic process at the population level. Here, we report high-throughput physiological phenotyping of water relations of 106 cowpea accessions under progressive drought stress, which, in combination of genome-wide association study (GWAS), enables genetic mapping of the complex, stomata-related drought responsive traits “critical soil water content” (θcri) and “slope of transpiration rate declining” (KTr). The 106 accessions showed large variations in θcri and KTr, indicating that they had broad spectrum of stomatal control in response to soil water deficit, which may confer them different levels of drought tolerance. Univariate GWAS identified six and fourteen significant SNPs associated with θcri and KTr, respectively. The detected SNPs distributed in nine chromosomes and accounted for 8.7–21% of the phenotypic variation, suggesting that both stomatal sensitivity to soil drought and the speed of stomatal closure to completion were controlled by multiple genes with moderate effects. Multivariate GWAS detected ten more significant SNPs in addition to confirming eight of the twenty SNPs as detected by univariate GWAS. Integrated, a final set of 30 significant SNPs associated with stomatal closure were reported. Taken together, our work, by combining phenomics and genetics, enables forward genetic mapping of the genetic architecture of stomatal traits related to drought tolerance, which not only provides a basis for molecular breeding of drought resistant cultivars of cowpea, but offers a new methodology to explore the genetic determinants of water budgeting in crops under stressful conditions in the phenomics era.

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The advantages of functional phenotyping in pre-field screening for drought-tolerant crops

Functional Plant Biology ◽

10.1071/fp16156 ◽

2017 ◽

Vol 44 (1) ◽

pp. 107 ◽

Cited By ~ 30

Author(s):

Boaz Negin ◽

Menachem Moshelion

Keyword(s):

Drought Tolerance ◽

Complex Traits ◽

Plant Stress ◽

Plant Responses ◽

Inappropriate Use ◽

Drought Tolerant ◽

Main Challenge ◽

Challenging Tasks ◽

Major Bottleneck ◽

High Throughput Phenotyping

Increasing worldwide demand for food, feed and fuel presents a challenge in light of limited resources and climatic challenges. Breeding for stress tolerance and drought tolerance, in particular, is one the most challenging tasks facing breeders. The comparative screening of immense numbers of plant and gene candidates and their interactions with the environment represents a major bottleneck in this process. We suggest four key components to be considered in pre-field screens (phenotyping) for complex traits under drought conditions: (i) where, when and under which conditions to phenotype; (ii) which traits to phenotype; (iii) how to phenotype (which method); and (iv) how to translate collected data into knowledge that can be used to make practical decisions. We describe some common pitfalls, including inadequate phenotyping methods, incorrect terminology and the inappropriate use of non-relevant traits as markers for drought tolerance. We also suggest the use of more non-imaging, physiology-based, high-throughput phenotyping systems, which, used in combination with soil–plant–atmosphere continuum (SPAC) measurements and fitting models of plant responses to continuous and fluctuating environmental conditions, should be further investigated in order to serve as a phenotyping tool to better understand and characterise plant stress response. In the future, we assume that many of today’s phenotyping challenges will be solved by technology and automation, leaving us with the main challenge of translating large amounts of accumulated data into meaningful knowledge and decision making tools.

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Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars

Frontiers in Genetics ◽

10.3389/fgene.2021.656037 ◽

2021 ◽

Vol 12 ◽

Author(s):

S. M. Hisam Al Rabbi ◽

Ajay Kumar ◽

Sepehr Mohajeri Naraghi ◽

Suraj Sapkota ◽

Mohammed S. Alamri ◽

...

Keyword(s):

Drought Tolerance ◽

Candidate Genes ◽

Phenotypic Variation ◽

Kernel Weight ◽

Snp Markers ◽

Expression Variability ◽

Volume Weight ◽

Drought Tolerant ◽

Ril Population ◽

Major Qtl

Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a high-yielding but drought-susceptible cultivar, ‘Albany.’ The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. In silico expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.

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Photochemical efficiency correlated with candidate gene expression promote coffee drought tolerance

Scientific Reports ◽

10.1038/s41598-021-86689-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Meline de Oliveira Santos ◽

Larissa Sousa Coelho ◽

Gladyston Rodrigues Carvalho ◽

Cesar Elias Botelho ◽

Luana Ferreira Torres ◽

...

Keyword(s):

Drought Tolerance ◽

Candidate Genes ◽

Water Deficit ◽

Water Status ◽

Photochemical Efficiency ◽

Regulatory Proteins ◽

Drought Tolerant ◽

Major Response ◽

Genes Expression ◽

Response To Stress

AbstractThe aim of this study was to identify the correlation between photochemical efficiency and candidate genes expression to elucidate the drought tolerance mechanisms in coffee progenies (Icatu Vermelho IAC 3851-2 × Catimor UFV 1602-215) previously identified as tolerant in field conditions. Four progenies (2, 5, 12 and 15) were evaluated under water-deficit conditions (water deficit imposed 8 months after transplanting seedlings to the pots) and under irrigated system. Evaluations of physiological parameters and expression of candidate genes for drought tolerance were performed. Progeny 5 showed capacity to maintain water potential, which contributed to lower qP variation between irrigated and deficit conditions. However, the increases of qN and NPQ in response to stress indicate that this progeny is photochemically responsive to small variations of Ψam protecting the photosystem and maintaining qP. Data obtained for progeny 12 indicated a lower water status maintenance capacity, but with increased qN and NPQ providing maintenance of the ɸPSII and ETR parameters. A PCA analysis revealed that the genes coding regulatory proteins, ABA-synthesis, cellular protectors, isoforms of ascorbate peroxidase clearly displayed a major response to drought stress and discriminated the progenies 5 and 12 which showed a better photochemical response. The genes CaMYB1, CaERF017, CaEDR2, CaNCED, CaAPX1, CaAPX5, CaGolS3, CaDHN1 and CaPYL8a were up-regulated in the arabica coffee progenies with greater photochemical efficiency under deficit and therefore contributing to efficiency of the photosynthesis in drought tolerant progenies.

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Does susceptibility to heat stress confound screening for drought tolerance in rice?

Functional Plant Biology ◽

10.1071/fp10224 ◽

2011 ◽

Vol 38 (4) ◽

pp. 261 ◽

Cited By ~ 28

Author(s):

Krishna S. V. Jagadish ◽

Jill E. Cairns ◽

Arvind Kumar ◽

Impa M. Somayanda ◽

Peter Q. Craufurd

Keyword(s):

Heat Stress ◽

Drought Tolerance ◽

Candidate Genes ◽

Tissue Temperature ◽

Drought Tolerant ◽

Hot Season ◽

Dry Seasons ◽

Drought And Heat Stress ◽

Drought Screening ◽

Mapping Populations

Drought affected rice areas are predicted to double by the end of this century, demanding greater tolerance in widely adapted mega-varieties. Progress on incorporating better drought tolerance has been slow due to lack of appropriate phenotyping protocols. Furthermore, existing protocols do not consider the effect of drought and heat interactions, especially during the critical flowering stage, which could lead to false conclusion about drought tolerance. Screening germplasm and mapping-populations to identify quantitative trait loci (QTL)/candidate genes for drought tolerance is usually conducted in hot dry seasons where water supply can be controlled. Hence, results from dry season drought screening in the field could be confounded by heat stress, either directly on heat sensitive processes such as pollination or indirectly by raising tissue temperature through reducing transpirational cooling under water deficit conditions. Drought-tolerant entries or drought-responsive candidate genes/QTL identified from germplasm highly susceptible to heat stress during anthesis/flowering have to be interpreted with caution. During drought screening, germplasm tolerant to water stress but highly susceptible to heat stress has to be excluded during dry and hot season screening. Responses to drought and heat stress in rice are compared and results from field and controlled environment experiments studying drought and heat tolerance and their interaction are discussed.

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High-throughput phenotyping platform for analyzing drought tolerance in rice

Planta ◽

10.1007/s00425-020-03436-9 ◽

2020 ◽

Vol 252 (3) ◽

Author(s):

Song Lim Kim ◽

Nyunhee Kim ◽

Hongseok Lee ◽

Eungyeong Lee ◽

Kyeong-Seong Cheon ◽

...

Keyword(s):

Drought Tolerance ◽

High Throughput ◽

Crop Production ◽

Near Infrared ◽

New Technologies ◽

Infrared Imaging ◽

Imaging Data ◽

Drought Tolerant ◽

Breeding Cycles ◽

High Throughput Phenotyping

Abstract Main conclusion A new imaging platform was constructed to analyze drought-tolerant traits of rice. Rice was used to quantify drought phenotypes through image-based parameters and analyzing tools. Abstract Climate change has increased the frequency and severity of drought, which limits crop production worldwide. Developing new cultivars with increased drought tolerance and short breeding cycles is critical. However, achieving this goal requires phenotyping a large number of breeding populations in a short time and in an accurate manner. Novel cutting-edge technologies such as those based on remote sensors are being applied to solve this problem. In this study, new technologies were applied to obtain and analyze imaging data and establish efficient screening platforms for drought tolerance in rice using the drought-tolerant mutant osphyb. Red–Green–Blue images were used to predict plant area, color, and compactness. Near-infrared imaging was used to determine the water content of rice, infrared was used to assess plant temperature, and fluorescence was used to examine photosynthesis efficiency. DroughtSpotter technology was used to determine water use efficiency, plant water loss rate, and transpiration rate. The results indicate that these methods can detect the difference between tolerant and susceptible plants, suggesting their value as high-throughput phenotyping methods for short breeding cycles as well as for functional genetic studies of tolerance to drought stress.

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Root and canopy traits and adaptability genes explain drought tolerance mechanism in winter wheat

10.1101/2020.11.04.367904 ◽

2020 ◽

Author(s):

A.S. Nehe ◽

M. J. Foulkes ◽

I. Ozturk ◽

A. Rasheed ◽

L. York ◽

...

Keyword(s):

Drought Tolerance ◽

Grain Yield ◽

High Throughput ◽

Vegetation Index ◽

Root Traits ◽

Wheat Cultivars ◽

Drought Tolerant ◽

Green Area ◽

High Throughput Phenotyping ◽

Semiarid Conditions

AbstractBread wheat (Triticum aestivum L) is one of main staple food crops worldwide contributing 20% calories in human diet. Drought stress is the main factor limiting yields and threatening to food security, with climate change resulting in more frequent and intense drought. Developing drought-tolerant wheat cultivars is a promising way forward. The use of a holistic approaches that include high-throughput phenotyping and genetic makers in selection could help in accelerating genetic gains. Fifty advanced breeding lines were selected from the CIMMYT Turkey winter wheat breeding program and studied under irrigated and semiarid conditions for two years. High-throughput phenotyping were done for wheat crown root traits using shovelomics techniques and canopy green area and senescence dynamics using vegetation indices (green area using RGB images and Normalized Difference Vegetation Index using spectral reflectance). In addition, genotyping by KASP markers for adaptability genes was done. Overall, under semiarid conditions compared to irrigated conditions yield reduced by 3.09 t ha−1 (−46.8%). Significant difference between the treatment and genotype was observed for grain yield and senescence traits. Genotypes responded differently under drought stress. Root traits including shallower nodal root angle under irrigated conditions and root number per shoot under semiarid conditions were associated with increased grain yield. RGB based vegetation index measuring canopy green area at anthesis was more strongly associated with GY than NDVI under drought. Five established functional genes (PRR73.A1 – flowering time, TEF-7A – grain size and weight, TaCwi.4A - yield under drought, Dreb1-drought tolerance, and ISBW11.GY.QTL.CANDIDATE- grain yield) were associated with different drought-tolerance traits in this experiment. We conclude that a combination of high-throughput phenotyping and selection for genetic markers can help to develop drought-tolerant wheat cultivars.

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