Genetic Basis for Lentil Adaptation to Summer Cropping in Northern Temperate Environments

ABSTRACTThe continued success of lentil (Lens culinaris Medik.) genetic improvement relies on the availability of broad genetic diversity and new alleles need to be identified and incorporated into the cultivated gene pool. Availability of robust and predictive markers greatly enhances the precise transfer of genomic regions from unadapted germplasm. Quantitative trait loci (QTLs) for key phenological traits in lentil were located using a recombinant inbreed line (RIL) population derived from a cross between an Ethiopian landrace (ILL 1704) and a northern temperate cultivar (CDC Robin). Field experiments were conducted at Sutherland research farm in Saskatoon and at Rosthern, Saskatchewan, Canada during 2018 and 2019. A linkage map was constructed using 21,634 SNPs located on seven linkage groups (LGs) which correspond to the seven haploid chromosomes of lentil. Eight QTL were identified for six phenological traits. Flowering related QTL were identified at two regions on LG6. FLOWERING LOCUS T (FT) genes were annotated within the flowering time QTL interval based on the lentil reference genome. Similarly, a major QTL for post-flowering developmental processes was located on LG5 with several senescence-associated genes annotated within the QTL interval. The flowering time QTL was validated in a different genetic background indicating the potential use of the identified markers for marker-assisted selection to precisely transfer genomic regions from exotic germplasm into elite crop cultivars without disrupting adaptation.Core IdeasStable QTL were located for key phenological traits in lentil that lead to regional adaptation.FT genes are candidates for controlling flowering time in lentil grown in temperate environments.A major locus controlling post-flowering developmental processes was located on lentil LG5 with several senescence-associated genes annotated within the QTL interval.Markers identified in this study can be useful for marker-assisted selection to precisely transfer genomic regions from exotic germplasm into elite lentil cultivars without disrupting adaptation.

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Prediction of root damaging during mechanical shaking of fruit trees

Progress in Agricultural Engineering Sciences ◽

10.1556/progress.10.2014.1 ◽

2014 ◽

Vol 10 (1) ◽

pp. 1-15

Author(s):

Z. Láng

Keyword(s):

Field Experiments ◽

Calculated Data ◽

Fruit Trees ◽

List Type ◽

Structure Model ◽

Root Damage ◽

Set Up ◽

Simple Tree ◽

The Given ◽

Cherry Trees

The possible effect of shaker harvest on root damage of 10-year-old cherry trees was studied on a simple tree structure model. The model was composed of elastic trunk and rigid main roots, the ends of which were connected to the surrounding soil via springs and dumping elements. Equations were set up to be able to calculate the relation between shaking height on the trunk and strain in the roots. To get the data for root break and their elongation at different shaking heights on the trunk, laboratory and field experiments were carried out on cherry trees and on their roots. Having evaluated the measured and calculated data it could be concluded that root damage is to be expected even at 3.6% strain and the risk of it increases with increased trunk amplitudes, i.e.with the decrease of shaking heightat smaller stem diameters (i.e. in younger plantation), andif the unbalanced mass of the shaker machine is too large for the given tree size.

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Mapping QTL for spike fertility and related traits in two doubled haploid wheat (Triticum aestivum L.) populations

BMC Plant Biology ◽

10.1186/s12870-021-03061-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nicole Pretini ◽

Leonardo S. Vanzetti ◽

Ignacio I. Terrile ◽

Guillermo Donaire ◽

Fernanda G. González

Keyword(s):

Doubled Haploid ◽

Marker Assisted Selection ◽

Triticum Aestivum L ◽

Physiological Model ◽

Yield Potential ◽

Breeding Programs ◽

Per Se ◽

Genomic Regions ◽

Fertility Traits ◽

Selection Of

Abstract Background In breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with higher grains per spike (GN) and occasionally increased grain weight (GW) (main numerical components of the yield). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two doubled haploid (DH) populations (Baguette Premium 11 × BioINTA 2002 and Baguette 19 × BioINTA 2002). Results In total 305 QTL were identified for 14 traits, out of which 12 QTL were identified in more than three environments and explained more than 10% of the phenotypic variation in at least one environment. Eight hotspot regions were detected on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B in which at least two major and stable QTL sheared confidence intervals. QTL on two of these regions (R5A.1 and R5A.2) have previously been described, but the other six regions are novel. Conclusions Based on the pleiotropic analysis within a robust physiological model we conclude that two hotspot genomic regions (R5A.1 and R5A.2) together with the QGW.perg-6B are of high relevance to be used in marker assisted selection in order to improve the spike yield potential. All the QTL identified for the spike related traits are the first step to search for their candidate genes, which will allow their better manipulation in the future.

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Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-082 ◽

2010 ◽

Vol 53 (11) ◽

pp. 884-898 ◽

Cited By ~ 31

Author(s):

Jianjun Zhao ◽

Anna Artemyeva ◽

Dunia Pino Del Carpio ◽

Ram Kumar Basnet ◽

Ningwen Zhang ◽

...

Keyword(s):

Association Mapping ◽

Flowering Time ◽

Brassica Rapa ◽

Core Collection ◽

Field Experiments ◽

Research Centre ◽

Candidate Gene Approach ◽

Core Collections ◽

Genome Wide ◽

Using Data

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

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Design and Evaluation of the Key Units in a Rapeseed Direct Seeder Integrated with Plowing-Rotating Combined Tillage

Applied Engineering in Agriculture ◽

10.13031/aea.14536 ◽

2021 ◽

Vol 37 (6) ◽

pp. 1005-1014

Author(s):

Guoliang Wei ◽

Qingsong Zhang ◽

Biao Wang ◽

QingXi Liao

Keyword(s):

Field Experiments ◽

Optimal Parameter ◽

Structural Parameters ◽

List Type ◽

Oil Crops ◽

Orthogonal Experiments ◽

Heavy Soil ◽

Tillage Depth ◽

Working Parameters ◽

Orthogonal Field

HighlightsThe seeder combined the plowing and rotating tillage to overcome the heavy soil and a large amount of straws.The plow could lift and turn the soil and straw before rotary tillage.The optimal working parameters of the seeder were obtained by orthogonal field experiments.Abstract. Rapeseed, one of the most important oil crops in China, is mainly planted in the mid-lower reaches of the Yangtze River. However, limited by the special long-term rice-rapeseed rotation, rotary tillage is applied in most of the planted areas apply instead of plow tillage, leading to a shallow arable layer. On the other hand, maintaining a high-quality seedbed for rapeseed becomes a challenge because a large amount of straw remains buried in the soil. As a solution, a rapeseed direct seeder that combines plow tillage and rotary tillage was designed. The structure of the plowing unit, whose key components were a lifting-turning plow and symmetrical plow, was analyzed based on the forming principle of the plow. Furthermore, a mechanical soil throwing model of the rotary tillage blade was built to determine the structural parameters. Then, the interaction between the rotary tillage unit and the lift-turning plow was analyzed. Finally, the performance and optimal parameters were evaluated by orthogonal field experiments. The seedbed after the operations indicated that the seeder could achieve the function of turning the soil and straw first and then rotating the soil with good passability, mixing the straw and the soil, flattening the surface of the seed bed, and stabilizing the tillage depth. Orthogonal experiments showed that the optimal working parameters of the seeder were as follows: the tillage depth was 180 mm, the equipment forward speed was 2.1 km/h, and the speed of the rotary tillage blade was 250 r/min. Under the optimal parameter combination, the power consumption of the seeder, the thickness of the tillage layer, the crop residue burial efficiency, the soil breakage efficiency, and the flatness of the seed bed surface were 30.48 kW, 231 mm, 90.88%, 93.26%, and 21.15 mm, respectively. The working performance of the seeder could meet the tillage requirements of rapeseed planting. Keywords: Direct seeder, Evaluation, Plow, Plowing-rotating combined tillage, Rapeseed.

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Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

10.21203/rs.2.24272/v1 ◽

2020 ◽

Author(s):

Aditi Bhandari ◽

Nitika Sandhu ◽

Jérôme Bartholome ◽

Tuong-Vi Cao-Hamadoun ◽

Nourollah Ahmadi ◽

...

Keyword(s):

Grain Yield ◽

Field Experiments ◽

Genome Wide Association Study ◽

Reproductive Stage ◽

Phenotypic Variance ◽

Rice Varieties ◽

Drought Tolerant ◽

Genome Wide ◽

Close Proximity ◽

Genomic Regions

Abstract Background Reproductive-stage drought stress is a major impediment to rice production globally. Conventional and marker-assisted breeding strategies for developing drought tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles and understanding their interactions with genetic backgrounds for contributing to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage drought. A diverse set of 280 indica-aus accessions was phenotyped for grain yield and nine yield-related traits under normal condition and under two managed drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 220 significant MTAs and candidate gene analysis within 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 47 genes, 4 earlier reported major grain yield QTLs and 8 novel QTLs for 10 traits. The significant MTAs were majorly located on chromosomes 1, 2, 5, 6, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related traits, except flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding program targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex-genetic architecture of grain yield under reproductive-stage drought under different environments. Validation of major genomic regions reported in the study can be effectively used to develop drought tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

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Genomic Regions Associated with the Control of Flowering Time in Durum Wheat

10.20944/preprints202010.0112.v1 ◽

2020 ◽

Author(s):

Priyanka Gupta ◽

Hafssa Kabbaj ◽

Khaoula El Hassouni ◽

Marco Maccaferri ◽

Miguel Sabchez-Garcia ◽

...

Keyword(s):

Durum Wheat ◽

Flowering Time ◽

Genome Wide Association Study ◽

Strong Association ◽

Triticum Aestivum L ◽

Day Length ◽

Significant Qtls ◽

A Genome ◽

Days To Heading ◽

Genomic Regions

Flowering time is a critical stage for crop development as it regulates the ability of plants to adapt to an environment. To understand the genetic control of flowering time, a genome wide association study (GWAS) was conducted to identify the genomic regions associated with the control of this trait in durum wheat (Triticum durum Desf.). A total of 96 landraces and 288 modern lines were evaluated for days to heading, growing degree days, and accumulated day length at flowering across 13 environments spread across Morocco, Lebanon, Mauritania, and Senegal. These environments were grouped into four pheno-environments based on temperatures, day length and other climatic variables. Genotyping with 35K Axiom array generated 7,652 polymorphic SNPs in addition to 3 KASP markers associated to known flowering genes. In total, 34 significant QTLs were identified in both landraces and modern lines. Some QTLs had strong association with already known regulatory photoperiod genes, Ppd-A and Ppd-B and vernalization genes Vrn-A1, and Vrn3. However, these loci explained only 5 to 20% of variance for days to heading. Seven QTLs overlapped between the two germplasm groups in which Q.ICD.Eps-03 and Q.ICD.Vrn-17 consistently affected flowering time in all the pheno-environments, while Q.ICD.Eps-11 and Q.ICD.Ppd-12 were significant only in two pheno-environments and the combined analysis across all environments. These results help clarify the genetic mechanism controlling flowering time in durum wheat and show some clear distinctions to what is known for common wheat (Triticum aestivum L.)

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Identification of Quantitative Trait Loci Relating to Flowering Time, Flag Leaf and Awn Characteristics in a Novel Triticum dicoccum Mapping Population

Plants ◽

10.3390/plants9070829 ◽

2020 ◽

Vol 9 (7) ◽

pp. 829

Author(s):

Tally I.C. Wright ◽

Angela C. Burnett ◽

Howard Griffiths ◽

Maxime Kadner ◽

James S. Powell ◽

...

Keyword(s):

Genetic Diversity ◽

Quantitative Trait Loci ◽

Flowering Time ◽

Quantitative Trait ◽

Marker Assisted Selection ◽

Mapping Population ◽

Flag Leaf ◽

Snp Array ◽

Leaf Length ◽

Trait Loci

Tetraploid landraces of wheat harbour genetic diversity that could be introgressed into modern bread wheat with the aid of marker-assisted selection to address the genetic diversity bottleneck in the breeding genepool. A novel bi-parental Triticum turgidum ssp. dicoccum Schrank mapping population was created from a cross between two landrace accessions differing for multiple physiological traits. The population was phenotyped for traits hypothesised to be proxies for characteristics associated with improved photosynthesis or drought tolerance, including flowering time, awn length, flag leaf length and width, and stomatal and trichome density. The mapping individuals and parents were genotyped with the 35K Wheat Breeders’ single nucleotide polymorphism (SNP) array. A genetic linkage map was constructed from 104 F4 individuals, consisting of 2066 SNPs with a total length of 3295 cM and an average spacing of 1.6 cM. Using the population, 10 quantitative trait loci (QTLs) for five traits were identified in two years of trials. Three consistent QTLs were identified over both trials for awn length, flowering time and flag leaf width, on chromosomes 4A, 7B and 5B, respectively. The awn length and flowering time QTLs correspond with the major loci Hd and Vrn-B3, respectively. The identified marker-trait associations could be developed for marker-assisted selection, to aid the introgression of diversity from a tetraploid source into modern wheat for potential physiological trait improvement.

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Landscape drivers and effectiveness of pest control by insectivorous birds in a landscape-dominant woody crop

10.1101/2020.03.07.981845 ◽

2020 ◽

Author(s):

Carlos Martínez-Núñez ◽

Pedro J. Rey ◽

Antonio J. Manzaneda ◽

Daniel García ◽

Rubén Tarifa ◽

...

Keyword(s):

Pest Control ◽

Ecosystem Service ◽

Field Experiments ◽

Landscape Heterogeneity ◽

List Type ◽

Insectivorous Birds ◽

Landscape Complexity ◽

Pest Damage ◽

Woody Crop ◽

Plasticine Models

AbstractAvian-mediated pest control is a significant ecosystem service with important economic implications. However, there is an overall paucity of experimental information about how landscape simplification affect its current level. Information on pest control by birds is missing in some permanent agroecosystems of worldwide importance, like olive orchards, that dominate vast areas in the Mediterranean region.We assess the effectiveness of insectivorous birds for controlling the two main pest insects in olive orchards and explore the effects of landscape complexity and distance to semi-natural patches on avian insectivore abundance and pest control. For this, we combine bird surveys with field experiments (branch exclusions and pest plasticine models) at the regional scale.Landscape heterogeneity increased the abundance and richness of insectivorous birds, which were also more abundant and diverse in semi-natural patches, compared to the farm olive matrix. Experiments evidenced that pest control by birds (measured as attack rates to plasticine models and pest damage) in the studied olive orchards is negligible, while pests were overall abundant and pest damage was high on most farms. This raises alarms about the status of avian pest control in this agroecosystem.Although landscape heterogeneity increased the abundance/richness of insectivorous birds, and favored some forest species, insectivorous bird abundance seems diluted in relation to prey availability in all landscapes. Thus, pest control by birds seems currently unsuccessful in olive orchards. Our results might be evidencing the loss of an ecosystem service due to a generalized massive decline of common and forest insectivorous birds.Key messageOlive orchards dominate extensive areas causing important landscape simplification.Insectivorous birds are more abundant in semi-natural patches within olive farms.Field experiments show a low impact of birds on olive pests and damage.Avian-mediated pest biocontrol seems diluted by limited suitable habitat for birds.Agri-environmental measures should focus on increasing landscape complexity.

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Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids

10.1101/188235 ◽

2017 ◽

Cited By ~ 1

Author(s):

Fanny Bonnafous ◽

Ghislain Fievet ◽

Nicolas Blanchet ◽

Marie-Claude Boniface ◽

Sébastien Carrère ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Flowering Time ◽

Genetic Control ◽

Quantitative Trait ◽

Complex Traits ◽

Association Studies ◽

Additive Models ◽

Genome Wide Association Studies ◽

Trait Loci ◽

Genomic Regions

AbstractGenome-wide association studies are a powerful and widely used tool to decipher the genetic control of complex traits. One of the main challenges for hybrid crops, such as maize or sunflower, is to model the hybrid vigor in the linear mixed models, considering the relatedness between individuals. Here, we compared two additive and three non-additive association models for their ability to identify genomic regions associated with flowering time in sunflower hybrids. A panel of 452 sunflower hybrids, corresponding to incomplete crossing between 36 male lines and 36 female lines, was phenotyped in five environments and genotyped for 2,204,423 SNPs. Intra-locus effects were estimated in multi-locus models to detect genomic regions associated with flowering time using the different models. Thirteen quantitative trait loci were identified in total, two with both model categories and one with only non-additive models. A quantitative trait loci on LG09, detected by both the additive and non-additive models, is located near a GAI homolog and is presented in detail. Overall, this study shows the added value of non-additive modeling of allelic effects for identifying genomic regions that control traits of interest and that could participate in the heterosis observed in hybrids.

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MOLECULAR MARKER ANALYSIS OF SPIKE FERTILITY INDEX AND RELATED TRAITS IN A BREAD WHEAT RECOMBINANT INBRED LINE POPULATION

Journal of Basic and Applied Genetics ◽

10.35407/bag.2019.xxx.02.01 ◽

2019 ◽

Vol 30 (2) ◽

pp. 7-20

Author(s):

J.S. Panelo ◽

M.P. Alonso ◽

N.E. Mirabella ◽

A.C. Pontaroli

Keyword(s):

Molecular Marker ◽

Field Experiments ◽

Bulked Segregant Analysis ◽

Functional Markers ◽

Grain Number ◽

Phenotypic Data ◽

Fertility Index ◽

Marker Analysis ◽

Molecular Marker Analysis ◽

Genomic Regions

Spike fertility index (SF) has been well established as an ecophysiological trait related to grain number per unit area and a promising selection target in wheat breeding programs. Scarce information on the molecular basis of SF is available thus far. In this study, a preliminary molecular marker analysis was carried out in a RIL population derived from the cross between two Argentinean cultivars with contrasting SF to identify candidate genomic regions associated with SF. Twenty-four microsatellites and two functional markers that had been found to co-segregate with SF in a bulked-segregant analysis of the F3 generation of the population were analyzed. Phenotypic data were collected from three field experiments carried out during 2013, 2014 and 2015 growing seasons at Balcarce, Argentina. Two genomic regions associated with SF in chromosomes 5BS and 7AS were detected, which merit further investigation. Key words: selection, genomic regions, grain number, yield, QTL, spike fertility index, fruiting efficiency

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