Novel major QTLs associated with low soil phosphorus tolerance identified from the Indian rice landrace, Wazuhophek

With an objective of mapping novel low soil P (Phosphorus) tolerance loci in the non-Pup1 type donor rice line, Wazuhophek, we screened a recombinant inbred line (RIL) mapping population consisting of 330 lines derived from the cross Wazuhophek x Improved Samba Mahsuri (which is highly sensitive to low soil P) in a plot with low soil P for tolerance associated traits. Molecular mapping with SSR markers revealed a total of 16 QTLs (seven major and nine minor QTLs), which are associated with low soil P tolerance related traits. Interestingly, a QTL hotspot, harbouring 10 out of 16 QTLs were identified on the short arm of chromosome 8 (flanked by the makers RM22554 and RM80005). Five major QTLs explaining phenotypic variance to an extent of 15.28%, 17.25%, 21.84%, 20.23%, and 18.50%, associated with the traits, plant height, shoot length, the number of productive tillers, panicle length and yield, respectively, were located in the hotspot. Two major QTLs located on chromosome 1, associated with the traits, total biomass and root to shoot ratio, explaining 15.44% and 15.44% phenotypic variance, respectively were also identified. Complex epistatic interactions were observed among the traits, grain yield per plant, days to 50% flowering, dry shoot weight, and P content of the seed. In-silico analysis of genomic regions flanking the major QTLs revealed the presence of key putative candidate genes, possibly associated with tolerance.

Download Full-text

Genotyping by sequencing for identification and mapping of QTLs for bioenergy-related traits in sweet sorghum

10.1101/2020.06.25.170662 ◽

2020 ◽

Author(s):

Kanokwan Teingtham ◽

David M. Braun ◽

Ismail Dweikat

Keyword(s):

Sweet Sorghum ◽

Recombinant Inbred Lines ◽

Genotyping By Sequencing ◽

Interval Mapping ◽

Chromosome 1 ◽

Total Biomass ◽

Sequencing Analysis ◽

Nucleotide Polymorphisms ◽

Sugar Transporter ◽

Major Qtls

AbstractSweet sorghum (Sorghum bicolor L. Moench) is a promising bioenergy crop. To increase the productivity of this crop, marker-assisted breeding will be important to advance genetic improvement of sweet sorghum. The objective of the present study was to identify quantitative trait loci (QTLs) associated with bioenergy-related traits in sweet sorghum. We used 188 F7 recombinant inbred lines (RILs) derived from a cross between sweet sorghum (Wray) and grain sorghum (Macia). The RILs and their parental lines were grown at two locations in 2012 and 2013. Genotyping-by-sequencing analysis of the RILs allowed the construction of a map with 979 single nucleotide polymorphisms. Using the inclusive composite interval mapping of additive QTLs, major QTLs for flowering time and head moisture content were detected on chromosome 6, and explained 29.45% and 20.65% of the phenotypic variances (PVE), respectively. Major QTLs for plant height (29.51% PVE) and total biomass yield (16.46% PVE) were detected on chromosome 7, and QTLs for stem diameter (9.43% PVE) and 100 seed weight (22.97% PVE) were detected on chromosome 1. A major QTL for brix (39.92% PVE) and grain yield (49.14%) PVE co-localized on chromosome 3, was detected consistently across four environments, and is closely associated with a SWEET sugar transporter gene. Additionally, several other QTLs for brix identified in this study or reported previously were found to be associated with sugar transporter genes. The identified QTLs in this study will help to further understand the underlying genes associated with bioenergy-related traits and could be used for development of molecular markers for marker-assisted selection.

Download Full-text

Molecular mapping of the chlorophyll retainer (cl) mutation in pepper (Capsicum spp.) and screening for candidate genes using tomato ESTs homologous to structural genes of the chlorophyll catabolism pathway

Genome ◽

10.1139/g04-119 ◽

2005 ◽

Vol 48 (2) ◽

pp. 347-351 ◽

Cited By ~ 26

Author(s):

Ari Efrati ◽

Yoram Eyal ◽

Ilan Paran

Keyword(s):

Expressed Sequence Tag ◽

Molecular Mapping ◽

Recessive Gene ◽

Chromosome 8 ◽

Chromosome 1 ◽

Structural Genes ◽

Chromosome 11 ◽

Pheophorbide A ◽

Catabolism Pathway ◽

Pheophorbide A Oxygenase

The chlorophyll retainer (cl) mutation causes inhibition of chlorophyll degradation during pepper fruit ripening and is controlled by a single recessive gene. The retention of chlorophyll in mature red or yellow fruits produces brown- or green-colored ripe fruits, respectively. We mapped CL on chromosome 1 of pepper corresponding to chromosome 8 in tomato in which a homologous mutation, green flesh, was previously assigned. To test whether known structural genes from the chlorophyll catabolism pathway could correspond to CL, we mapped tomato expressed sequence tag clones corresponding to three loci of CHLOROPHYLLASE and one locus of PHEOPHORBIDE A OXYGENASE in the tomato introgression lines population. The three CHLOROPHYLLASE loci mapped to chromosomes 6, 9, and 12, while PHEOPHORBIDE A OXYGENASE mapped to chromosome 11, indicating that CL may correspond to an as yet unavailable gene from the chlorophyll catabolism pathway or to a regulator of the pathway.Key words: fruit color, pepper, tomato, molecular mapping, chlorophyll catabolism.

Download Full-text

Molecular Mapping of QTLs for Heat Tolerance in Chickpea

International Journal of Molecular Sciences ◽

10.3390/ijms19082166 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2166 ◽

Cited By ~ 25

Author(s):

Pronob Paul ◽

Srinivasan Samineni ◽

Mahendar Thudi ◽

Sobhan Sajja ◽

Abhishek Rathore ◽

...

Keyword(s):

Heat Stress ◽

Heat Tolerance ◽

Molecular Mapping ◽

Recombinant Inbred Lines ◽

Interval Mapping ◽

Snp Markers ◽

Environment Interaction ◽

Major Qtls ◽

Heat Tolerant ◽

Genomic Regions

Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL × environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea.

Download Full-text

QTL Mapping of Panicle Architecture and Yield-related Traits Between Two U.S. Rice Cultivars ‘LaGrue’ and ‘Lemont’

10.21203/rs.3.rs-299812/v1 ◽

2021 ◽

Author(s):

Adam Rice ◽

Dustin North ◽

Karen Ann-Kuenzel Moldenhauer ◽

Andy Pereira ◽

Ainong Shi ◽

...

Keyword(s):

Candidate Genes ◽

Agronomic Traits ◽

Block Design ◽

Chromosome 8 ◽

Chromosome 1 ◽

Yield Traits ◽

Rice Cultivars ◽

Major Qtls ◽

Panicle Number ◽

Number Of Seeds

Abstract Grain yield is a quantitative trait that is determined by several agronomic traits. Unfortunately, there is little information about the genetics behind yield components in U.S. rice cultivars. The objective of the study were to 1) conduct a QTL study for identification of chromosome regions associated with yield traits in two US developed rice cultivars and 2) identify candidate genes in major QTL regions related to yield traits. Four rice cultivars were evaluated in the summer 2017 at the University of Arkansas System Division of Agriculture’s Rice Research and Extension Center (RREC) at Stuttgart, AR for 15 agronomic traits associated with yield. Of the four cultivars, “LaGrue” had a higher number of seeds/panicle, number of primary panicle branches/panicle, and number of seeds/plant and “Lemont”, despite having longer panicles and higher 100 seed weight/panicle, produced the least number of seeds among the cultivars. A bi-parental population was developed from a cross between LaGrue and Lemont for QTL analysis. Leaf samples from F2 plants were collected for genetic analysis. A set of 322 F2:3 lines were evaluated in a randomized complete block design (RCBD) for several agronomic traits at two locations with three replications for each line. A total of 17 major QTLs were detected including two major QTLs for plant height on chromosome 1 and two major QTLs for flag leaf length and panicle length on chromosome 8 with seven candidate genes found in these regions. The results from the study would be useful for marker assisted selection in rice breeding.

Download Full-text

Genomic regions associated with chocolate spot (Botrytis fabae Sard.) resistance in faba bean (Vicia faba L.)

10.1101/2021.11.22.469473 ◽

2021 ◽

Author(s):

Tadesse S. Gela ◽

Margaret Bruce ◽

Wei Chang ◽

Frederick L. Stoddard ◽

Alan H. Schulman ◽

...

Keyword(s):

Disease Resistance ◽

Faba Bean ◽

Snp Markers ◽

Chromosome 1 ◽

Phenotypic Variance ◽

Resistance Qtls ◽

Climate Conditions ◽

Botrytis Fabae ◽

Chocolate Spot ◽

Genomic Regions

Chocolate spot (CS), caused by Botrytis fabae Sard., is an important threat to global faba bean production. Growing resistant faba bean cultivars is, therefore, paramount to preventing yield loss. To date, there have been no reported quantitative trait loci (QTLs) associated with CS resistance in faba bean. The objective of this study was to identify genomic regions associated with CS resistance using a recombinant inbred line (RIL) population derived from resistant accession ILB 938. A total of 165 RILs from the cross between Melodie/2 and ILB 938/2 were genotyped and evaluated for CS reactions under replicated, controlled climate conditions. QTL analysis identified five loci contributing to CS resistance on faba bean chromosomes 1 and 6, accounting for 5.0-23.4% of the total phenotypic variance. The sequences of SNP markers linked to resistance QTLs on chromosome 1 that have the largest effects encode multiple classes of putative disease and/or defense-related genes. The results of this study not only provide insight into disease-resistance QTLs, but can also be used as potential targets for marker-assisted breeding in faba bean genetic improvement for CS resistance. Keywords: Botrytis fabae; chocolate spot; faba bean; disease resistance; QTL mapping; candidate gene

Download Full-text

Improved Plant Diversity as a Strategy to Increase Available Soil Phosphorus

10.24047/bc103143 ◽

2019 ◽

Vol 103 (1) ◽

pp. 43-45 ◽

Cited By ~ 1

Author(s):

Carlos Crusciol ◽

João Rigon ◽

Juliano Calonego ◽

Rogério Soratto

Keyword(s):

Crop Yields ◽

Soil Phosphorus ◽

Cropping System ◽

P Availability ◽

P Fractions ◽

Crop Species ◽

Soil P ◽

Residue Decomposition ◽

Available Soil Phosphorus ◽

Crop Residue Decomposition

Some crop species could be used inside a cropping system as part of a strategy to increase soil P availability due to their capacity to recycle P and shift the equilibrium between soil P fractions to benefit the main crop. The release of P by crop residue decomposition, and mobilization and uptake of otherwise recalcitrant P are important mechanisms capable of increasing P availability and crop yields.

Download Full-text

Roles of Phosphate Solubilizing Microorganisms from Managing Soil Phosphorus Deficiency to Mediating Biogeochemical P Cycle

Biology ◽

10.3390/biology10020158 ◽

2021 ◽

Vol 10 (2) ◽

pp. 158

Author(s):

Jiang Tian ◽

Fei Ge ◽

Dayi Zhang ◽

Songqiang Deng ◽

Xingwang Liu

Keyword(s):

Phosphorus Deficiency ◽

Soil Phosphorus ◽

Biological Molecules ◽

P Deficiency ◽

Soil P ◽

Soil Systems ◽

Intensively Managed ◽

Phosphate Solubilizing ◽

P Fertilizers ◽

P Cycle

Phosphorus (P) is a vital element in biological molecules, and one of the main limiting elements for biomass production as plant-available P represents only a small fraction of total soil P. Increasing global food demand and modern agricultural consumption of P fertilizers could lead to excessive inputs of inorganic P in intensively managed croplands, consequently rising P losses and ongoing eutrophication of surface waters. Despite phosphate solubilizing microorganisms (PSMs) are widely accepted as eco-friendly P fertilizers for increasing agricultural productivity, a comprehensive and deeper understanding of the role of PSMs in P geochemical processes for managing P deficiency has received inadequate attention. In this review, we summarize the basic P forms and their geochemical and biological cycles in soil systems, how PSMs mediate soil P biogeochemical cycles, and the metabolic and enzymatic mechanisms behind these processes. We also highlight the important roles of PSMs in the biogeochemical P cycle and provide perspectives on several environmental issues to prioritize in future PSM applications.

Download Full-text

Effect of mixed cropping and plant extracts on the growth, yield and pest control of jute (Corchorus olitorius L.)

Folia Horticulturae ◽

10.2478/fhort-2013-0006 ◽

2013 ◽

Vol 25 (1) ◽

pp. 49-60 ◽

Cited By ~ 5

Author(s):

Adeyela I. Okunlola ◽

Thomas I. Ofuya

Keyword(s):

Plant Extracts ◽

Growth And Yield ◽

Total Biomass ◽

Percentage Increase ◽

Mixed Cropping ◽

Corchorus Olitorius ◽

Marketable Yield ◽

Piper Guineense ◽

Shoot Weight ◽

Number Of Branches

ABSTRACT This study investigated the effect of plant extracts (Azadirachta indica and Piper guineense) on the growth and yield of jute (Corchorus olitorius L.) (Cor) under sole and mixed cropping with Amaranthus hybridus (Ama) and Celosia argentea (Cel). The highest percentage increase in plant height, number of leaves, number of branches and stem girth (130.6, 865.0, 220.4 and 114.0%, respectively) was found in untreated Cor + Cel, cypermethrin treated Cor + Ama, cypermethrin treated Cor and A. indica extract treated Cor + Ama, respectively. The highest percentage increase in shoot weight (71.0%), marketable yield (53.9%) and total biomass (51.5%) was in A. indica treated C. olitorius. Extract treatment had no effect on the number of branches at four, five and seven weeks after planting (WAP) in Cor + Ama + Cel; four, five and six WAP in Cor + Cel; four and six WAP in Cor + Ama; as well as four and five WAP in Cor. The highest percentage increase in leaf fresh weight was obtained in cypermethrin treated Cor (53.3%) and Cor + Ama + Cel (52.2%), while the smallest increase was in P. guineense treated Cor (1.1%) and Cor + Ama (2.5%). The activity of A. indica was independent of time of application while P. guineense was not. Among the extract treated groups, the highest percentage increase in shoot weight (71.0%), marketable yield (53.9%) and total biomass (51.5%) was in A. indica treated Cor. The activity of the extracts against insect pests of sole cropped Cor increased significantly (p < 0.05) with increasing extract concentration. The highest efficiency with the use of P. guineense was 250 g dm-3 at four, five and six WAP (94.0, 92.7 and 90.3%, respectively) and 200 mg dm-3 at seven WAP (81.7%). In the case of A. indica extract, the highest efficiency was found with the use of 200 g dm-3 at four, six and seven WAP (92.7, 85.3 and 100%, respectively). A. indica extract (250 g dm-3) treatment gave the highest efficiency at five WAP (100%).

Download Full-text

Soil phosphorus availability and soybean response to phosphorus starter fertilizer

Revista Brasileira de Ciência do Solo ◽

10.1590/s0100-06832014000500014 ◽

2014 ◽

Vol 38 (5) ◽

pp. 1487-1495 ◽

Cited By ~ 3

Author(s):

Ciro Antonio Rosolem ◽

Alexandre Merlin

Keyword(s):

Soil Phosphorus ◽

Soil Surface ◽

Tropical Soils ◽

P Fertilization ◽

Soil P ◽

Brachiaria Ruziziensis ◽

Soluble P ◽

Surface Spread ◽

P Sources

Phosphorus fixation in tropical soils may decrease under no-till. In this case, P fertilizer could be surface-spread, which would improve farm operations by decreasing the time spend in reloading the planter with fertilizers. In the long term, less soluble P sources could be viable. In this experiment, the effect of surface-broadcast P fertilization with both soluble and reactive phosphates on soil P forms and availability to soybean was studied with or without fertilization with soluble P in the planting furrow in a long-term experiment in which soybean was grown in rotation with Ruzigrass (Brachiaria ruziziensis). No P or 80 kg ha-1 of P2O5 in the form of triple superphosphate or Arad reactive rock phosphate was applied on the surface of a soil with variable P fertilization history. Soil samples were taken to a depth of 60 cm and soil P was fractionated. Soybean was grown with 0, 30, and 60 kg ha-1 of P2O5 in the form of triple phosphate applied in the seed furrow. Both fertilizers applied increased available P in the uppermost soil layers and the moderately labile organic and inorganic forms of P in the soil profile, probably as result of root decay. Soybean responded to phosphates applied on the soil surface or in the seed furrow; however, application of soluble P in the seed furrow should not be discarded. In tropical soils with a history of P fertilization, soluble P sources may be substituted for natural reactive phosphates broadcast on the surface. The planting operation may be facilitated through reduction in the rate of P applied in the planting furrow in relation to the rates currently applied.

Download Full-text

Relationship between Yield Components and Partial Resistance to Lecanicillium fungicola in the Button Mushroom, Agaricus bisporus, Assessed by Quantitative Trait Locus Mapping

Applied and Environmental Microbiology ◽

10.1128/aem.07554-11 ◽

2012 ◽

Vol 78 (7) ◽

pp. 2435-2442 ◽

Cited By ~ 23

Author(s):

Marie Foulongne-Oriol ◽

Anne Rodier ◽

Jean-Michel Savoie

Keyword(s):

Quantitative Trait ◽

Wild Strain ◽

Genomic Region ◽

Yield Component ◽

Phenotypic Variance ◽

Button Mushroom ◽

Content Type ◽

Dry Bubble ◽

Trait Locus ◽

Genomic Regions

ABSTRACTDry bubble, caused byLecanicillium fungicola, is one of the most detrimental diseases affecting button mushroom cultivation. In a previous study, we demonstrated that breeding for resistance to this pathogen is quite challenging due to its quantitative inheritance. A second-generation hybrid progeny derived from an intervarietal cross between a wild strain and a commercial cultivar was characterized forL. fungicolaresistance under artificial inoculation in three independent experiments. Analysis of quantitative trait loci (QTL) was used to determine the locations, numbers, and effects of genomic regions associated with dry-bubble resistance. Four traits related to resistance were analyzed. Two to four QTL were detected per trait, depending on the experiment. Two genomic regions, on linkage group X (LGX) and LGVIII, were consistently detected in the three experiments. The genomic region on LGX was detected for three of the four variables studied. The total phenotypic variance accounted for by all QTL ranged from 19.3% to 42.1% over all traits in all experiments. For most of the QTL, the favorable allele for resistance came from the wild parent, but for some QTL, the allele that contributed to a higher level of resistance was carried by the cultivar. Comparative mapping with QTL for yield-related traits revealed five colocations between resistance and yield component loci, suggesting that the resistance results from both genetic factors and fitness expression. The consequences for mushroom breeding programs are discussed.

Download Full-text