scholarly journals Mapping freezing tolerance QTL in alfalfa: based on indoor phenotyping

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Laxman Adhikari ◽  
Shiva O. Makaju ◽  
Orville M. Lindstrom ◽  
Ali M. Missaoui
Keyword(s):  
Cold Tolerance ◽  
Freezing Tolerance ◽  
Screening Method ◽  
Freezing Temperature ◽  
Indirect Selection ◽  
Selection Method ◽  
Snp Markers ◽  
Winter Hardiness ◽  
Close Relative ◽  
Percentage Survival

Abstract Background Winter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were tested for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping-by-sequencing (GBS) and the quantitative trait loci (QTL) associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild. Results Alfalfa FT screening method optimized in this experiment comprises three major steps: clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is a useful indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL associated with four traits; nine for visual rating-based FT, five for percentage survival (PS), four for treated to control regrowth ratio (RR), and two for treated to control biomass ratio (BR). Some QTL positions overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) were from the potential genic region for a cold tolerance gene CBF. The BLAST alignment of a CBF sequence of M. truncatula, a close relative of alfalfa, against the alfalfa reference showed that the gene’s ortholog resides around 75 Mb on chromosome 6. Conclusions The indoor freezing tolerance selection method reported is useful for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources for the research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement.

scholarly journals Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping

2020 ◽  
Author(s):  
Laxman Adhikari ◽  
Shiva O. Makaju ◽  
Orville M. Lindstrom ◽  
Ali Mekki Missaoui
Keyword(s):  
Cold Tolerance ◽  
Freezing Tolerance ◽  
Screening Method ◽  
Genotyping By Sequencing ◽  
Freezing Temperature ◽  
Indirect Selection ◽  
Selection Method ◽  
Snp Markers ◽  
Winter Hardiness ◽  
Percentage Survival

Abstract Background Winter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were phenotyped for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping by sequencing (GBS) and the QTL associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild. Results Alfalfa FT screening method optimized in this experiment comprises three major steps; clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is useful as an indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL for four traits; visual rating-based FT, percentage survival (PS), treated to control regrowth ratio (RR), and treated to control biomass ratio (BR). Some QTL overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) potentially represented the genic region of a cold tolerance gene, the c-repeat binding factor (CBF). These QTL were located on the terminal end of chromosome 6 which is considered a location of the CBF homologs in alfalfa.Conclusions The indoor freezing tolerance selection method reported here is valuable for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources needed by the alfalfa research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement.

scholarly journals Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Luomiao Yang ◽  
Jingguo Wang ◽  
Zhenghong Han ◽  
Lei Lei ◽  
Hua Long Liu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Regulatory Gene ◽  
Snp Markers ◽  
Seedling Stage ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Coding Region ◽  
Rice Varieties ◽  
Major Qtl

Abstract Background Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular rice breeding. Results In this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9°C/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice. Conclusion We identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.

scholarly journals Transcriptome Analysis of Distinct Cold Tolerance Strategies in the Rubber Tree (Hevea brasiliensis)

2018 ◽  
Author(s):  
Camila Campos Mantello ◽  
Lucas Boatwright ◽  
Carla Cristina da Silva ◽  
Erivaldo Jose Scaloppi ◽  
Paulo de Souza Gonçalves ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Hevea Brasiliensis ◽  
Amazon Basin ◽  
Rubber Tree ◽  
Tree Breeding ◽  
Snp Markers ◽  
Large Field ◽  
New Variety ◽  
Cold Response ◽  
Cold Temperatures

AbstractNatural rubber is an indispensable commodity used in approximately 40,000 products and is fundamental to the tire industry. Among the species that produce latex, the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg.], a species native to the Amazon rainforest, is the major producer of latex used worldwide. The Amazon Basin presents optimal conditions for rubber tree growth, but the occurrence of South American leaf blight, which is caused by the fungus Microcyclus ulei (P. Henn) v. Arx, limits rubber tree production. Currently, rubber tree plantations are located in scape regions that exhibit suboptimal conditions such as high winds and cold temperatures. Rubber tree breeding programs aim to identify clones that are adapted to these stress conditions. However, rubber tree breeding is time-consuming, taking more than 20 years to develop a new variety. It is also expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. Transcriptome sequencing using next-generation sequencing (RNA-seq) is a powerful tool to identify a full set of transcripts and for evaluating gene expression in model and non-model species. In this study, we constructed a comprehensive transcriptome to evaluate the cold response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes. Furthermore, we identified putative microsatellite (SSR) and single-nucleotide polymorphism (SNP) markers. Alternative splicing, which is an important mechanism for plant adaptation under abiotic stress, was further identified, providing an important database for further studies of cold tolerance.

scholarly journals INDIRECT SELECTION OF FEMALE TROUT AS A SELECTION METHOD TO INCREASE THEIR PRODUCTIVITY AND RESISTANCE

2020 ◽  
pp. 180-186
Author(s):  
I.N. Agleev ◽  
◽  
А.V. Bushov ◽  
Keyword(s):  
Live Weight ◽  
Indirect Selection ◽  
Selection Method ◽  
The Body ◽  
Oxygen Absorption ◽  
Control Group ◽  
Head Region ◽  
Functional Features ◽  
Experimental Group ◽  
Selection Of

The scientific work considers the selection method of selection in a herd of producers of rainbow trout Kamloops, taking into account values of positive correlation of some morphometric characteristics and degree of development of their reproductive products, as well as the features of natural protective functions of their body at the age of three. It is established that the somatic structure and, development of postorbital region largely determine the functional features of trout, as well as their reproductive qualities. In the indirect selection of three-year-old breeders, taking into account morphometry and correlation, females with a size of postorbital head region greater than 55 mm exceeded by 29.2% the live weight and by 40.4% the weight of trout caviar with a length of this head region less than 55 mm. When comparing the resistance of two experimental groups of three-year-old breeder flock, certain differences in immune proteins and hemoglobin content in blood were revealed. Note that in the selected group of fish, a large degree of saturation of red blood cells with hemoglobin is observed, which indicates increased share of oxygen absorption by the body, as well as the intensity of redox processes of metabolism. Indicators of serum proteins of trout in experimental groups vary ambiguously. So in the experimental group, producers had an average total protein in blood of 63.26 g / l, which is significantly 17.5% more than in the blood of fish in the control group. This can be explained by the relationship of the globulins with the immune status of fish of experimental group and its resistance by raising the level of globulin fraction, a high amount of Ig M` protein (by 42.9%) in the blood of trout in the experimental group suggests more aggressive immune system in these fish to viral, invasive and other infections, indicating improved adaptability of selected herds.

Traits Measured on Seedlings Can Be Used to Select for Later Volume of Loblolly Pine

1984 ◽  
Vol 8 (1) ◽  
pp. 59-63
Author(s):  
John F. Robinson ◽  
J. P. Van Buijtenen ◽  
Ernest M. Long
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Indirect Selection ◽  
Selection Method ◽  
Southeast Texas ◽  
Selection For ◽  
Pinus Taeda L ◽  
Individual Trees ◽  
Seed Characteristics ◽  
Seedling Characteristics

Abstract Seed was collected from individual trees in loblolly pine (Pinus taeda L.) stands in southeast Texas. Although selection on seed characteristics proved ineffective as an indirect selection method for improving five-year volume, selection for seedling characteristics prior to outplanting proved very effective. Families selected in greenhouse and nursery beds averaged 36 percent greater volume after five years in the field than checklots from the same stands. Seed from the southernmost stands produced more volume than seed from more northern stands. Seed weights of selected families were significantly greater than those of appropriate checks.

Winter Hardiness and Freezing Tolerance in a Hairy Vetch Collection

Crop Science ◽  
2018 ◽  
Vol 58 (4) ◽  
pp. 1594-1604 ◽  
Author(s):  
Nicholas P. Wiering ◽  
Claire Flavin ◽  
Craig C. Sheaffer ◽  
Garett C. Heineck ◽  
Walid Sadok ◽  
...  
Keyword(s):  
Freezing Tolerance ◽  
Winter Hardiness ◽  
Hairy Vetch

scholarly journals Balancing selection maintains diversity in a cold tolerance gene in broadly distributed live oaks

Genome ◽  
2017 ◽  
Vol 60 (9) ◽  
pp. 762-769 ◽  
Author(s):  
Jose Eduardo Meireles ◽  
Anne Beulke ◽  
Daniel S. Borkowski ◽  
Jeanne Romero-Severson ◽  
Jeannine Cavender-Bares
Keyword(s):  
Cold Acclimation ◽  
Cold Tolerance ◽  
Freezing Tolerance ◽  
Negative Selection ◽  
Balancing Selection ◽  
Variable Temperature ◽  
Purifying Selection ◽  
Housekeeping Genes ◽  
Cold Response ◽  
Tolerance Gene

Cold poses major physiological challenges to plants, especially long-lived trees. In trees occurring along variable temperature clines, the expected direction and consequences of selection on cold acclimation ability and freezing tolerance are not straightforward. Here we estimated selection in cold acclimation genes at two evolutionary timescales in all seven species of the American live oaks (Quercus subsection Virentes). Two cold response candidate genes were chosen: ICE1, a key gene in the cold acclimation pathway, and HOS1, which modulates cold response by negatively regulating ICE1. Two housekeeping genes, GAPDB and CHR11, were also analyzed. At the shallow evolutionary timescale, we demonstrate that HOS1 experienced recent balancing selection in the two most broadly distributed species, Q. virginiana and Q. oleoides. At a deeper evolutionary scale, a codon-based model of evolution revealed the signature of negative selection in ICE1. In contrast, three positively selected codons have been identified in HOS1, possibly a signature of the diversification of Virentes into warmer climates from a freezing adapted lineage of oaks. Our findings indicate that evolution has favored diversity in cold tolerance modulation through balancing selection in HOS1 while maintaining core cold acclimation ability, as evidenced by purifying selection in ICE1.

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