Definition of Soybean Genomic Regions That Control Seed Phytoestrogen Amounts

Soybean seeds contain large amounts of isoflavones or phytoestrogens such as genistein, daidzein, and glycitein that display biological effects when ingested by humans and animals. In seeds, the total amount, and amount of each type, of isoflavone varies by 5 fold between cultivars and locations. Isoflavone content and quality are one key to the biological effects of soy foods, dietary supplements, and nutraceuticals. Previously we had identified 6 loci (QTL) controlling isoflavone content using 150 DNA markers. This study aimed to identify and delimit loci underlying heritable variation in isoflavone content with additional DNA markers. We used a recombinant inbred line (RIL) population (n=100) derived from the cross of “Essex” by “Forrest,” two cultivars that contrast for isoflavone content. Seed isoflavone content of each RIL was determined by HPLC and compared against 240 polymorphic microsatellite markers by one-way analysis of variance. Two QTL that underlie seed isoflavone content were newly discovered. The additional markers confirmed and refined the positions of the six QTL already reported. The first new region anchored by the marker BARC-Satt063 was significantly associated with genistein (P=0.009,R2=29.5%) and daidzein (P=0.007,R2=17.0%). The region is located on linkage group B2 and derived the beneficial allele from Essex. The second new region defined by the marker BARC-Satt129 was significantly associated with total glycitein (P=0.0005,R2=32.0%). The region is located on linkage group D1a+Q and also derived the beneficial allele from Essex. Jointly the eight loci can explain the heritable variation in isoflavone content. The loci may be used to stabilize seed isoflavone content by selection and to isolate the underlying genes.

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Genomic Regions That Underlie Soybean Seed Isoflavone Content

Journal of Biomedicine and Biotechnology ◽

10.1155/s1110724301000110 ◽

2001 ◽

Vol 1 (1) ◽

pp. 38-44 ◽

Cited By ~ 51

Author(s):

K. Meksem ◽

V. N. Njiti ◽

W. J. Banz ◽

M. J. Iqbal ◽

My. M. Kassem ◽

...

Keyword(s):

Linkage Group ◽

High Performance ◽

Biological Effects ◽

Recombinant Inbred Lines ◽

Soybean Seed ◽

Soybean Seeds ◽

Isoflavone Content ◽

Seed Isoflavone ◽

Genomic Regions

Soy products contain isoflavones (genistein, daidzein, and glycitein) that display biological effects when ingested by humans and animals, these effects are species, dose and age dependent. Therefore, the content and quality of isoflavones in soybeans is a key to their biological effect. Our objective was to identify loci that underlie isoflavone content in soybean seeds. The study involved 100 recombinant inbred lines (RIL) from the cross of ‘Essex’ by ‘Forrest,’ two cultivars that contrast for isoflavone content. Isoflavone content of seeds from each RIL was determined by high performance liquid chromatography (HPLC). The distribution of isoflavone content was continuous and unimodal. The heritability estimates on a line mean basis were 79% for daidzein, 22% for genistein, and 88% for glycitein. Isoflavone content of soybean seeds was compared against 150 polymorphic DNA markers in a one-way analysis of variance. Four genomic regions were found to be significantly associated with the isoflavone content of soybean seeds across both locations and years. Molecular linkage group B1 contained a major QTL underlying glycitein content (P=0.0001,R 2=50.2%), linkage groupNcontained a QTL for glycitein (P=0.0033,R 2=11.1%) and a QTL for daidzein (P=0.0023,R 2=10.3%) and linkage groupA1contained a QTL for daidzein (P=0.0081,R 2=9.6%). Selection for these chromosomal regions in a marker assisted selection program will allow for the manipulation of amounts and profiles of isoflavones (genistein, daidzein, and glycitein) content of soybean seeds. In addition, tightly linked markers can be used in map based cloning of genes associated with isoflavone content.

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A single linkage group comprising 11 polymorphic DNA markers on rat Chromosome 3

Mammalian Genome ◽

10.1007/bf00354926 ◽

1994 ◽

Vol 5 (9) ◽

pp. 538-541 ◽

Cited By ~ 9

Author(s):

H. Zha ◽

E. F. Remmers ◽

Y. Du ◽

E. A. Goldmuntz ◽

P. Mathern ◽

...

Keyword(s):

Linkage Group ◽

Dna Markers ◽

Chromosome 3 ◽

Single Linkage

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Molecular loci associated with seed isoflavone content may underlie resistance to soybean pod borer (Leguminivora glycinivorella)

Plant Breeding ◽

10.1111/pbr.12233 ◽

2015 ◽

Vol 134 (1) ◽

pp. 78-84 ◽

Cited By ~ 4

Author(s):

Guiyun Zhao ◽

Zhenfeng Jiang ◽

Dongmei Li ◽

Yingpeng Han ◽

Haibo Hu ◽

...

Keyword(s):

Pod Borer ◽

Isoflavone Content ◽

Seed Isoflavone

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Genetic control of soybean seed isoflavone content: importance of statistical model and epistasis in complex traits

Theoretical and Applied Genetics ◽

10.1007/s00122-009-1109-z ◽

2009 ◽

Vol 119 (6) ◽

pp. 1069-1083 ◽

Cited By ~ 52

Author(s):

Juan Jose Gutierrez-Gonzalez ◽

Xiaolei Wu ◽

Juan Zhang ◽

Jeong-Dong Lee ◽

Mark Ellersieck ◽

...

Keyword(s):

Statistical Model ◽

Genetic Control ◽

Complex Traits ◽

Soybean Seed ◽

Isoflavone Content ◽

Seed Isoflavone

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The genetic and RFLP characterization of the left end of linkage group III in Caenorhabditis elegans

Genome ◽

10.1139/g93-096 ◽

1993 ◽

Vol 36 (4) ◽

pp. 712-724 ◽

Cited By ~ 2

Author(s):

Dave Pilgrim

Keyword(s):

Caenorhabditis Elegans ◽

Linkage Group ◽

Genetic Map ◽

Physical Map ◽

Group Iii ◽

C Elegans ◽

Genomic Regions ◽

Caenorhabditis Elegans Genome ◽

Selection Of

A genetic approach was taken to identify new transposable element Tc1 -dependent polymorphisms on the left end of linkage group III in the nematode Caenorhabditis elegans. The cloning of the genomic DNA surrounding the Tc1 allowed the selection of overlapping clones (from the collection being used to assemble the physical map of the C. elegans genome). A contig of approximately 600–800 kbp in the region has been identified, the genetic map of the region has been refined, and 10 new RFLPs as well as at least four previously characterized genetic loci have been positioned onto the physical map, to the resolution of a few cosmids. This analysis demonstrated the ability to combine physical and genetic mapping for the rapid analysis of large genomic regions (0.5–1 Mbp) in genetically amenable eukaryotes.Key words: Caenorhabditis elegans, genome analysis, RFLP, physical map, genetic map.

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Identification and validation of quantitative trait loci controlling seed isoflavone content across multiple environments and backgrounds in soybean

Molecular Breeding ◽

10.1007/s11032-017-0768-8 ◽

2017 ◽

Vol 38 (1) ◽

Cited By ~ 3

Author(s):

Xihuan Li ◽

Samson Kamala ◽

Rui Tian ◽

Hui Du ◽

Wenlong Li ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Isoflavone Content ◽

Trait Loci ◽

Multiple Environments ◽

Seed Isoflavone

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Genotyping Porcine Circovirus 3 (PCV-3) Nowadays: Does It Make Sense?

Viruses ◽

10.3390/v12030265 ◽

2020 ◽

Vol 12 (3) ◽

pp. 265 ◽

Cited By ~ 7

Author(s):

Giovanni Franzo ◽

Eric Delwart ◽

Robert Fux ◽

Ben Hause ◽

Shuo Su ◽

...

Keyword(s):

Genetic Distance ◽

Complete Genome ◽

Molecular Data ◽

Porcine Circovirus ◽

Bootstrap Support ◽

Research Activity ◽

Reading Frame ◽

Porcine Circovirus 3 ◽

Definition Of ◽

Genomic Regions

The discovery of a globally distributed porcine circovirus (Porcine circovirus 3; PCV-3) has led to intense research activity and the production of a large amount of molecular data. Different research groups have proposed several, not always concordant, genotypes for this virus. While such categories could aid an easier interpretation of PCV-3 molecular epidemiology, any classification, to be useful in practical settings, must be univocal and of help in the understanding of underlying biological features and epidemiology. Based on these premises, the possibility of defining PCV-3 genotypes was evaluated on the broadest available dataset of PCV-3 complete genome (n = 357) and open reading frame 2 (ORF2, n = 653) sequences. Genetic distance and phylogenetic clustering were selected as the main objective criteria. Additional factors, including the number of within-cluster sequences, host and geographic clustering, concordance between different genomic regions, and analysis method were also taken in account to generate a classification that could be effectively applied in research and diagnostic settings. A maximum within-genotype genetic distance of 3% at the complete genome and 6% at the ORF2 levels, bootstrap support higher than 90%, and concordance between analysis methods allowed us to clearly define two clades which could be potentially defined as genotypes. Further subdivision was not suggested due to the absence of a meaningful association between PCV-3 and its biological/epidemiological features. Nevertheless, since one of the clades included two strains only, thus far we formally propose the definition of only one PCV-3 genotype (PCV-3a). The established criteria will allow us to automatically recognize other genotypes when more strain sequences are characterized.

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Multiple Disease Resistance Loci Affect Soilborne Disease Resistance in Tobacco (Nicotiana tabacum)

Phytopathology ◽

10.1094/phyto-03-17-0118-r ◽

2017 ◽

Vol 107 (9) ◽

pp. 1055-1061 ◽

Cited By ~ 8

Author(s):

Katherine Drake-Stowe ◽

Nicolas Bakaher ◽

Simon Goepfert ◽

Berangere Philippon ◽

Regis Mark ◽

...

Keyword(s):

Disease Resistance ◽

Dna Markers ◽

Phytophthora Nicotianae ◽

Soilborne Pathogens ◽

High Positive Correlation ◽

Soilborne Disease ◽

Breeding Populations ◽

Multiple Disease Resistance ◽

Phytophthora Resistance ◽

Genomic Regions

Phytophthora nicotianae and Ralstonia solanacearum are two of the most important pathogens affecting tobacco worldwide. Greater insight regarding genetic systems controlling resistance to these two soilborne pathogens, as well as identification of DNA markers associated with genomic regions controlling this resistance, could aid in variety development. An evaluation of 50 historical tobacco lines revealed a high positive correlation between resistances to the two pathogens, preliminarily suggesting that some genomic regions may confer resistance to both pathogens. A quantitative trait loci (QTL) mapping experiment designed to investigate the genetic control of soilborne disease resistance of highly resistant ‘K346’ tobacco identified four QTL significantly associated with resistance to P. nicotianae (explaining 60.0% of the observed phenotypic variation) and three QTL to be associated with R. solanacearum resistance (explaining 50.3% of the observed variation). The two QTL with the largest effect on Phytophthora resistance were also found to be the QTL with the greatest effects on resistance to Ralstonia. This finding partially explains previously observed associations between resistances to these two pathogens among U.S. current cultivars and within breeding populations. Further study is needed to determine whether these relationships are due to the same genes (i.e., pleiotropy) or favorable coupling-phase linkages that have been established over time.

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Genomics: the host's genotype and its relevance to bovine respiratory disease

Animal Health Research Reviews ◽

10.1017/s1466252320000134 ◽

2020 ◽

pp. 1-5

Author(s):

Holly Neibergs

Keyword(s):

Dairy Cattle ◽

Respiratory Disease ◽

Bovine Respiratory Disease ◽

Genomic Variation ◽

National Standards ◽

Host Susceptibility ◽

Association Analyses ◽

Heritability Estimates ◽

Definition Of ◽

Genomic Regions

Abstract Genomic variation exists in cattle that affects their susceptibility to the complex of pathogens responsible for bovine respiratory disease (BRD). Heritability estimates and genome-wide association analyses (GWAA) support the role of host genomic variation in BRD susceptibility. Heritability estimates for BRD susceptibility range from 0.02 to 0.29 depending on the population, the definition of the disease, and the accuracy of diagnosis. GWAA have identified genomic regions (loci) associated with BRD in beef and dairy cattle based on a variety of BRD diagnostic criteria. National standards need to be developed for BRD diagnostics and reporting to facilitate selection. Commercial genotyping is available to predict BRD susceptibility in dairy cattle and for the selection of replacement animals. Disease pathogen profiles vary by region and can result in genetic heterogeneity where different loci are important for susceptibility to different BRD pathogens. Although the identification of the BRD pathogens may not be critical for treatment, it is of paramount importance in identifying loci that render cattle susceptible to the disease. Identification of loci associated with host susceptibility to BRD provides a foundation for genomic selection to reduce disease and opens the possibilities to a better understanding of how the host defends itself.

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