An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily

Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species—date palm (Phoenix dactylifera L.) and coconut palm (Cocos nucifera L.)—confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of Arecoideae, which consists of 107 species belonging to Arecaceae.

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High-throughput phenotyping reveals a link between transpiration efficiency and transpiration restriction under high evaporative demand and new loci controlling water use-related traits in African rice, Oryza glaberrima Steud.

10.1101/2021.11.28.470237 ◽

2021 ◽

Author(s):

Pablo Affortit ◽

Branly Effa Effa ◽

Mame Sokhatil Ndoye ◽

Daniel Moukouanga ◽

Nathalie Luchaire ◽

...

Keyword(s):

Water Use Efficiency ◽

Water Use ◽

Association Studies ◽

Crop Improvement ◽

Oryza Glaberrima ◽

Genome Wide Association Studies ◽

Transpiration Efficiency ◽

Evaporative Demand ◽

African Rice ◽

Use Efficiency

Because water availability is the most important environmental factor limiting crop production, improving water use efficiency, the amount of carbon fixed per water used, is a major target for crop improvement. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand, remain unknown. These traits were measured in a panel of 147 African rice Oryza glaberrima genotypes, known as potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly differentiated genotypes confirmed these associations and suggested that the root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency and its residuals, that links to genes involved in water transport and cell wall patterning. Our data suggest that root shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.

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Meta-Analysis Reveals Consensus Genomic Regions Associated with Multiple Disease Resistance in Wheat ( Triticum Aestivum L.)

10.21203/rs.3.rs-773587/v1 ◽

2021 ◽

Author(s):

Dinesh Kumar Saini ◽

Amneek Chahal ◽

Neeraj Pal ◽

Puja Srivast ◽

Pushpendra Kumar Gupta

Keyword(s):

Disease Resistance ◽

Physical Map ◽

Association Studies ◽

Meta Analysis ◽

Septoria Tritici Blotch ◽

Septoria Tritici ◽

Karnal Bunt ◽

Genome Wide Association Studies ◽

Head Blight ◽

Multiple Disease Resistance

Abstract In wheat, meta-QTLs (MQTLs), and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103; fusarium head blight (FHB), 184; karnal bunt (KB), 66, and loose smut (LS), 14. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of initial QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed genes (DEGs). Among the DEGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping of MDR genes and marker-assisted breeding.

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Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato

Biology ◽

10.3390/biology8040090 ◽

2019 ◽

Vol 8 (4) ◽

pp. 90 ◽

Cited By ~ 7

Author(s):

Juhi Chaudhary ◽

Praveen Khatri ◽

Pankaj Singla ◽

Surbhi Kumawat ◽

Anu Kumari ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Tolerance ◽

Association Studies ◽

Abiotic Stress Tolerance ◽

Crop Improvement ◽

Genetic Regulatory Networks ◽

Plant Responses ◽

Genome Wide Association Studies ◽

Market Demand ◽

Efficient Utilization

Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring due to biotic as well as abiotic stresses. Although tomato is a temperate crop, it is grown in almost all the climatic zones because of widespread demand, which makes it challenge to adapt in diverse conditions. Development of tomato cultivars with enhanced abiotic stress tolerance is one of the most sustainable approaches for its successful production. In this regard, efforts are being made to understand the stress tolerance mechanism, gene discovery, and interaction of genetic and environmental factors. Several omics approaches, tools, and resources have already been developed for tomato growing. Modern sequencing technologies have greatly accelerated genomics and transcriptomics studies in tomato. These advancements facilitate Quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). However, limited efforts have been made in other omics branches like proteomics, metabolomics, and ionomics. Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism. The information provided here will be helpful to understand the plant responses and the genetic regulatory networks involved in abiotic stress tolerance and efficient utilization of omics resources for tomato crop improvement.

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Bud Rot Caused by Phytophthora palmivora: A Destructive Emerging Disease of Oil Palm

Phytopathology ◽

10.1094/phyto-09-15-0243-rvw ◽

2016 ◽

Vol 106 (4) ◽

pp. 320-329 ◽

Cited By ~ 36

Author(s):

G. A. Torres ◽

G. A. Sarria ◽

G. Martinez ◽

F. Varon ◽

A. Drenth ◽

...

Keyword(s):

Oil Palm ◽

Plant Pathogens ◽

Elaeis Guineensis ◽

Cocos Nucifera ◽

Phytophthora Palmivora ◽

Economic Implications ◽

Irish Famine ◽

Palm Species ◽

Great Irish Famine ◽

The Tropics

Oomycetes from the genus Phytophthora are among the most important plant pathogens in agriculture. Epidemics caused by P. infestans precipitated the great Irish famine and had a major impact on society and human history. In the tropics, P. palmivora is a pathogen of many plant species including cacao (Theobroma cacao), citrus (Citrus sp.), durian (Durio zibethines), jackfruit (Artrocarpus heterophyllus), rubber (Hevea brasiliensis), and several palm species including coconut (Cocos nucifera), and the African oil palm (Elaeis guineensis) as determined recently. The first localized epidemics of bud rot in oil palm in Colombia were reported in 1964. However, recent epidemics of bud rot have destroyed more than 70,000 ha of oil palm in the Western and Central oil palm growing regions of Colombia. The agricultural, social, and economic implications of these outbreaks have been significant in Colombia. Identification of the pathogen after 100 years of investigating the disease in the world enabled further understanding of infection, expression of a range of symptoms, and epidemiology of the disease. This review examines the identification of P. palmivora as the cause of bud rot in Colombia, its epidemiology, and discusses the importance of P. palmivora as a major threat to oil palm plantings globally.

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SSR Marker Based Genetic Diversity Analysis and SNP Haplotyping of Genes Associating Abiotic and Biotic Stress Tolerance, Rice Growth and Development and Yield Across 93 Rice Landraces

10.21203/rs.3.rs-466659/v1 ◽

2021 ◽

Author(s):

Smitha Kunhiraman Vasumathy ◽

Manickavelu Alagu

Keyword(s):

Genetic Diversity ◽

Stress Tolerance ◽

Growth And Development ◽

Haplotype Analysis ◽

Association Studies ◽

Abiotic Stress Tolerance ◽

Crop Improvement ◽

World Population ◽

Genome Wide Association Studies ◽

Rice Landraces

Abstract I. Background: As rice is the staple food for more than half of the world population, enhancing grain yield irrespective of the variable climatic conditions is indispensable. Many of the traditionally cultivated rice landraces are well adapted to severe environmental conditions and have high genetic diversity that could play an important role in crop improvement.II. Methods and Results: The present study disclosed high level of genetic diversity among the unexploited rice landraces cultivated by farmers of Kerala. Twelve polymorphic markers detected a total of seventy- seven alleles with an average of 6.416 alleles per locus. PIC value ranged from 0.459 to 0.809 and to differentiate the rice genotypes, RM 242 was found to be the most appropriate marker with the highest value of 0.809. The current study indicated that the rice landraces were highly diverse with higher values of the effective number of alleles, PIC, and Shannon information index and utilizing these informative SSR markers for future molecular characterization and population genetic studies in rice landraces are advisable. Haplotypes are sets of genomic regions within a chromosome that are inherited together and haplotype-based breeding is a promising strategy for designing next-generation rice varieties. Here, haplotype analysis explored 270 haplotype blocks and 775 haplotypes from all the chromosomes of landraces under study. The number of SNPs in each haplotype block ranged from two to 28. Haplotypes of genes related to biotic and abiotic stress tolerance, yield-enhancing, and growth and development in rice landraces were also elucidated in the current study.III. Conclusions: The present investigation revealed genetic diversity of rice landraces and the haplotype analysis will open the way for genome wide association studies, QTL identification, and marker assisted selection in the unexplored rice landraces collected from Kerala.

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Trapping-a major tactic of BIPM strategy of palm weevils

CORD ◽

10.37833/cord.v21i01.401 ◽

2005 ◽

Vol 21 (01) ◽

pp. 34 ◽

Cited By ~ 1

Author(s):

S. P. Singh ◽

P. Rethinam

Keyword(s):

Tamil Nadu ◽

Date Palm ◽

Elaeis Guineensis ◽

Cocos Nucifera ◽

Middle Eastern ◽

Phoenix Dactylifera ◽

Economic Losses ◽

Palm Species ◽

The Status ◽

Cocos Nucifera L

Several species of curculionid weevils such as Amerrhinus ynca Sahlberg, Cholus annulatus Linnaeus, C. martiniquensis Marshall, C. zonatus (Swederus), Diocalandra frumenti (Fabricius), Dynamis borassi Fabricius, Homalinotus coriaceus Gyllenhal, Metamasius hemipterus Linnaeus, Paramasius distortus (Gemminger & Horold), Rhabdoscelus obscurus (Boisduval), Rhinostomus barbirostris (Fabricius), R. afzelii (Gyllenhal), Rhynchophorus bilineatus (Montrouzier), R. cruentatus Fabricius, R. ferrugineus (Olivier), R. palmarum (Linnaeus) and R. phoenicis (Fabricius) are associated with palms. Some of these have become a major constraint in the successful cultivation of coconut palm (Cocos nucifera L.), date palm (Phoenix dactylifera L.) and oil palm (Elaeis guineensis L.). R. ferrugineus is distributed in over 33 countries and attacks more than two dozen palm species. In the recent past, it has spread to Middle Eastern countries, Mediterranean region of Africa and southern Europe (Spain) causing tremendous economic losses. The yield of date palm has decreased from 10 to 0.7 tons/ha. Coconut palms in India are infested upto 6.9 per cent in Kerala and 11.65 per cent in Tamil Nadu. R. palmarum is a major pest of oil and coconut palms in the tropical Americas and, vectors the nematode, Bursaphelenchus cocophilus (Cobb) Baujard which causes red ring disease (RRD). Palm losses due to RRD are commonly between 0.1 to 15% which amounts to tens of millions dollars. The status of other species is briefed. The grubs of weevils that develop in the stems, bud, rachis of leaves and inflorescence of cultivated, ornamental or wild palms cause direct damage. Because of the cryptic habitat of the grubs, which act as tissue borer, the management becomes difficult.

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Comprehensive analysis and genome-wide association studies of biomass, chlorophyll, seed and salinity tolerance related traits in rice highlight genetic hotspots for crop improvement

10.1101/2020.12.24.424354 ◽

2020 ◽

Author(s):

Md Nafis Ul Alam ◽

G.M. Nurnabi Azad Jewel ◽

Tomalika Azim ◽

Zeba I. Seraj

Keyword(s):

Candidate Genes ◽

Sequence Data ◽

Expression Profiles ◽

Association Studies ◽

Crop Improvement ◽

Gene Expression Profiles ◽

Fixed Effect Model ◽

Specific Gene ◽

Genome Wide Association Studies ◽

Multiple Trait

AbstractFarmland is on the decline and worldwide food security is at risk. Rice is the staple of choice for over half the Earth’s people. To sustain current demands and ascertain a food secure future, substandard farmland affected by abiotic stresses must be utilized. For rapid crop improvement, a broader understanding of polygenic traits like stress tolerance and crop yield is indispensable. To this end, the hidden diversity of resilient and neglected wild varieties must be traced back to their genetic roots. In this study, we separately assayed 15 phenotypes in a panel of 176 diverse accessions predominantly comprised of local landraces from Bangladesh. We compiled high resolution sequence data for these accessions. We collectively studied the ties between the observed phenotypic differences and the examined additive genetic effects underlying these variations. We applied a sophisticated fixed effect model to associate phenotypes with genotypes on a genomic scale. Discovered QTLs were mapped to known genes. Candidate genes were sorted by tissue specific gene expression profiles and protein level consequence of existing polymorphisms. Our explorations yielded 17 QTLs related to various traits in multiple trait classes. 12 identified QTLs were equivalent to findings from previous studies. Integrative analysis assumes novel functionality for 21 candidate genes on multiple evidence levels. These findings will usher novel avenues for the bioengineering of high yielding crops of the future fortified with genetic defenses against abiotic stressors.

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Causal Haplotype Block Identification in Plant Genome-Wide Association Studies

10.1101/2021.10.28.466332 ◽

2021 ◽

Author(s):

Xing Wu ◽

Wei Jiang ◽

Christopher Fragoso ◽

Jing Huang ◽

Geyu Zhou ◽

...

Keyword(s):

Fine Mapping ◽

Complex Traits ◽

Haplotype Block ◽

Association Studies ◽

Crop Improvement ◽

Plant Genome ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Haplotype Blocks ◽

Genome Wide

Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) used in many GWAS that marginally test single nucleotide polymorphisms (SNPs) have successfully identified many loci with major and minor effects. In plants, the relatively small population size in GWAS and the high genetic diversity found many plant species can impede mapping efforts on complex traits. Here we present a novel haplotype-based trait fine-mapping framework, HapFM, to supplement current GWAS methods. HapFM uses genotype data to partition the genome into haplotype blocks, identifies haplotype clusters within each block, and then performs genome-wide haplotype fine-mapping to infer the causal haplotype blocks of trait. We benchmarked HapFM, GEMMA, BSLMM, and GMMAT in both simulation and real plant GWAS datasets. HapFM consistently resulted in higher mapping power than the other GWAS methods in simulations with high polygenicity. Moreover, it resulted in higher mapping resolution, especially in regions of high LD, by identifying small causal blocks in the larger haplotype block. In the Arabidopsis flowering time (FT10) datasets, HapFM identified four novel loci compared to GEMMA results, and its average mapping interval of HapFM was 9.6 times smaller than that of GEMMA. In conclusion, HapFM is tailored for plant GWAS to result in high mapping power on complex traits and improved mapping resolution to facilitate crop improvement.

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Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean

Genetics ◽

10.1534/genetics.120.303038 ◽

2020 ◽

Vol 215 (1) ◽

pp. 267-284 ◽

Cited By ~ 8

Author(s):

Alice H. MacQueen ◽

Jeffrey W. White ◽

Rian Lee ◽

Juan M. Osorno ◽

Jeremy Schmutz ◽

...

Keyword(s):

Common Bean ◽

Association Studies ◽

Crop Improvement ◽

Genetic Research ◽

The United States ◽

Genetic Effects ◽

Genome Wide Association Studies ◽

Genetic Associations ◽

Phenotypic Data ◽

Genomic Regions

Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for > 70 years in the United States and Canada, consisting of 20–50 entries each year at 10–20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement.

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