QTL mapping using GBS and SSR genotyping reveals genomic regions controlling wheat coleoptile length and seedling emergence

Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

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Explaining the heritability of an ecologically significant trait in terms of individual quantitative trait loci

Biology Letters ◽

10.1098/rsbl.2011.0409 ◽

2011 ◽

Vol 7 (6) ◽

pp. 896-898 ◽

Cited By ~ 13

Author(s):

Alison G. Scoville ◽

Young Wha Lee ◽

John H. Willis ◽

John K. Kelly

Keyword(s):

Qtl Mapping ◽

Quantitative Trait ◽

Complex Traits ◽

Genetic Variance ◽

Balancing Selection ◽

Natural Populations ◽

Population Based ◽

Population Variation ◽

Trait Locus ◽

Genomic Regions

Most natural populations display substantial genetic variation in behaviour, morphology, physiology, life history and the susceptibility to disease. A major challenge is to determine the contributions of individual loci to variation in complex traits. Quantitative trait locus (QTL) mapping has identified genomic regions affecting ecologically significant traits of many species. In nearly all cases, however, the importance of these QTLs to population variation remains unclear. In this paper, we apply a novel experimental method to parse the genetic variance of floral traits of the annual plant Mimulus guttatus into contributions of individual QTLs. We first use QTL-mapping to identify nine loci and then conduct a population-based breeding experiment to estimate V Q , the genetic variance attributable to each QTL. We find that three QTLs with moderate effects explain up to one-third of the genetic variance in the natural population. Variation at these loci is probably maintained by some form of balancing selection. Notably, the largest effect QTLs were relatively minor in their contribution to heritability.

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SELECTION FOR IMPROVED SEEDLING VIGOR IN RUSSIAN WILD RYEGRASS

Canadian Journal of Plant Science ◽

10.4141/cjps84-016 ◽

1984 ◽

Vol 64 (1) ◽

pp. 131-138 ◽

Cited By ~ 10

Author(s):

J. D. BERDAHL ◽

R. E. BARKER

Keyword(s):

Seed Weight ◽

Seedling Emergence ◽

Field Tests ◽

Visual Assessment ◽

Seedling Vigor ◽

Coleoptile Length ◽

Stand Establishment ◽

Psathyrostachys Juncea ◽

Emergence Percentage ◽

Selection For

Seedling emergence of 30 open-pollinated progeny lines of Russian wild ryegrass (Psathyrostachys juncea (Fisch.) Nevski. Syn: Elymus junceus Fisch.) ranging in seed weight from 2.1 to 4.5 mg/seed was evaluated in laboratory and greenhouse tests and compared to stand establishment capability in the field. Increases in emergence percentage and coleoptile length associated with increased seed weight diminished when seed weights of parents increased beyond 3.0 mg/seed. Emergence in two field environments was correlated with emergence from a 5-cm planting depth in the greenhouse (r = 0.70** and 0.71** for field tests 1 and 2, respectively) and with coleoptile length (r = 0.51** and 0.64**), but not with emergence under laboratory-induced drought stress of −1.1 MPa matric potential (r = −0.05 and 0.13). Experimental error was high for measurements of forage yields in the establishment year (CV = 38% and 36% for field tests 1 and 2, respectively), and resources required to obtain reliable yields would limit testing to a small number of entries. Preliminary screening of a Russian wild ryegrass population for improved seedling vigor could be accomplished by first eliminating plants with small seed size by visual assessment of seed samples. This could then be followed by selection for increased coleoptile length among progeny lines from those plants with medium or large seed.Key words: Russian wild ryegrass, seedling vigor, stand establishment, seed weight, coleoptile length

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QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance

Theoretical and Applied Genetics ◽

10.1007/s00122-012-2003-7 ◽

2012 ◽

Vol 126 (3) ◽

pp. 583-600 ◽

Cited By ~ 55

Author(s):

Gustavo Dias Almeida ◽

Dan Makumbi ◽

Cosmos Magorokosho ◽

Sudha Nair ◽

Aluízio Borém ◽

...

Keyword(s):

Drought Tolerance ◽

Qtl Mapping ◽

Tropical Maize ◽

Maize Populations ◽

Genomic Regions

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Identification of genomic regions and candidate genes associated with growth ofEriocheir Sinensisby QTL mapping and marker annotation

Aquaculture Research ◽

10.1111/are.12878 ◽

2015 ◽

Vol 48 (1) ◽

pp. 246-258 ◽

Cited By ~ 4

Author(s):

Min Hui ◽

Zhaoxia Cui ◽

Yuan Liu ◽

Chengwen Song ◽

Yingdong Li ◽

...

Keyword(s):

Qtl Mapping ◽

Candidate Genes ◽

Genomic Regions

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Relationship Between Coleoptile Length and Drought Resistance and Their QTL Mapping in Rice

Rice Science ◽

10.1016/s1672-6308(07)60003-1 ◽

2007 ◽

Vol 14 (1) ◽

pp. 13-20 ◽

Cited By ~ 12

Author(s):

Song-ping HU ◽

Hua YANG ◽

Gui-hua ZOU ◽

Hong-yan LIU ◽

Guo-lan LIU ◽

...

Keyword(s):

Qtl Mapping ◽

Drought Resistance ◽

Coleoptile Length

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Genomic regions and underlying candidate genes associated with coleoptile length under deep sowing conditions in a wheat RIL population

Journal of Plant Biochemistry and Biotechnology ◽

10.1007/s13562-014-0277-3 ◽

2014 ◽

Vol 24 (3) ◽

pp. 324-330 ◽

Cited By ~ 8

Author(s):

Kalpana Singh ◽

Sanyukta Shukla ◽

Suhas Kadam ◽

Vimal Kumar Semwal ◽

Nagendra Kumar Singh ◽

...

Keyword(s):

Candidate Genes ◽

Coleoptile Length ◽

Ril Population ◽

Genomic Regions

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Effect of Natural Seed Aging on Root and Shoot Traits in Bread Wheat (Triticum aestivum L.) Cultivars

Turkish Journal of Agriculture - Food Science and Technology ◽

10.24925/turjaf.v9i4.759-763.4158 ◽

2021 ◽

Vol 9 (4) ◽

pp. 759-763

Author(s):

Hayati Akman

Keyword(s):

Bread Wheat ◽

Germination Rate ◽

Seedling Emergence ◽

Seed Storage ◽

Wheat Cultivars ◽

Coleoptile Length ◽

Seed Aging ◽

Long Term Storage ◽

Term Storage

This study targeted to elucidate the effect of seed aging on germination and emergence rates with and shoot characteristics in wheat cultivars. For this purpose, different bread wheat cultivars stored for 7 years and non-stored were compared for coleoptile length, root mass, shoot mass, root length as well as germination and seedling emergence rates. Here, the evidence suggested that seed storage over a prolonged period affected root and Shoot growth, coleoptile length, seed germination, and seedling emergence rates adversely. By linking germination and emergence rates, the data presented here indicated that a reduction in emergence rate in long-term storage was higher than that in the germination rate. It was also found that there were significant variations among the wheat cultivars about investigated traits during long-term storage. However, the emergence rates of Kate A1 and Flamura 85 were not affected substantially by long-term storage. The study suggested future studies to focus on clarification of the process controlling natural seed aging as such knowledge allows clue the eventual consequences of long-term storage.

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Inhibitory impact of Daraikh (Melia Azedarach) leaves litter on wheat (Triticum aestivum) seedling

JOURNAL OF WEED SCIENCE RESEARCH ◽

10.28941/pjwsr.v27i2.876 ◽

2021 ◽

Vol 27 (2) ◽

pp. 191-200

Author(s):

Iqtidar Hussain

Keyword(s):

Triticum Aestivum ◽

Negative Impact ◽

Seedling Emergence ◽

Dry Weight ◽

Inhibitory Effect ◽

Germination Percentage ◽

Melia Azedarach ◽

Growth Stages ◽

Initial Growth ◽

Coleoptile Length

A biological phenomenon by which one plant releases some chemicals in the environment that affect the rate of germination, its seedling emergence and physiology and overall growth of neighboring plants is called allelopathy. The significance of study was checked allelopathic phytochemical potential of Daraikh (Melia Azedarach L.) leaves on Wheat. Leaves litter were used to examine the allelopathic effects of Daraikh (Melia Azedarach) at five concentrations (100, 200, 300, 400 g, control) parameters studied germination percentage (%), Speed of germination, plant height (cm), root length (cm), Shoot length (cm), coleoptile length (cm), Fresh weight (g) and dry weight (g), Tiller (plant-1) and chlorophyll content (µ cm-2) of Triticum aestivum. All concentration of Leaves litter of Melia Azedarach showed pronounced inhibitory effect on all parameters of Triticum aestivum. Melia Azedarach exerted phytotoxic influence on Triticum aestivum at initial growth stages. Melia Azedarach exhibited a significant negative impact on germination of Triticum aestivum at 100, 200, 300, 400 g litter of leaves than control (Sterilized soil) repectively. Melia Azedarach halted the coleoptile length of Triticum aestivum @ 400 g leaves litter. Powdered leaves of Melia Azedarach in clay loam soil appeared to have strong allelopathic inhibition under maximum concentrations on growth and germination of Triticum aestivum. Hence, Melia Azedarach proved a strong allelopathic plant that should be planted aside from field to avoid harmful impacts during early growth stages of Triticum aestivum.

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