Novel QTL for Low Seed Cadmium Accumulation in Soybean

Nissan, Nour; Hooker, Julia; Pattang, Arezo; Charette, Martin; Morrison, Malcolm J.; Yu, Kangfu; Hou, Anfu; Golshani, Ashkan; Molnar, Stephen J.; Cober, Elroy R.; Samanfar, Bahram

doi:10.3390/plants11091146

Cited by 3 publications

(3 citation statements)

References 47 publications

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“…In our screening, results obtained with this marker, were identical to the ones obtained with the SSR marker Sack149, respectively, all the genotypes with the digested PCR product being classified into the low Cd-accumulation type group. Another approach for the screening of soybean germplasm, regarding the classification into low or high Cd-accumulation, was the KASP assay with a marker developed by Nissan et al (2022).…”

Section: Resultsmentioning

confidence: 99%

“…The KASP primers (development by Nissan et al, 2022) carry a standard FAM tail (5′-GAAGGTGACCAAGTTCATGCT-3′) and HEX tail (5′-GAAGGTCGGAGTCAACG GATT-3′) with different fluorescence signals.…”

Section: Dna Amplificationmentioning

confidence: 99%

“…This researchers team developed a derived cleaved amplified polymorphic sequence (dCAPS) marker to detect the base substitution, and this dCAPS marker was successfully associated with seed Cd concentration. Recently, Nissan et al (2022), developed a KASP (Kompetitive Allele Specific PCR) marker, based on the SNP sequence, for efficient marker-assisted breeding for Cda1. Also, in the same study, a novel minor QTL was identified on chromosome 13 in the X4050 population between SSR markers Satt522 and Satt218.…”

Section: Introductionmentioning

confidence: 99%

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Screening Soybean Germplasm for Presence of Cda1 Allele Involved in Low Cadmium Accumulation Using Molecular Markers

Ciucă¹,

Cristina²,

Petcu³

et al. 2023

RAR

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Soybean is an important source of plant protein used in human diets. Cadmium (Cd) from agricultural soil is a toxic metal for plants, including soybean. Furthermore, the cadmium is taken up to seeds of soybean and becomes a risk for animals and human by feed and food chain. A method to avoid this risk is represented by the selection and breeding soybean lines/cultivars with genetic potential to minimized cadmium accumulation. This work reports an approach assisted by DNA-markers for selection of soybean cultivars with low Cd-accumulation. In this study, we screened the alleles of Cda1 gene, in 22 soybean cultivars, using three DNA markers (SSR-Sack149, Gm-dCAPS-HMA1 and Cda1-KASP). The results showed that 11 genotypes carried the allele for low cadmium accumulation, 8 genotypes had the allele for high cadmium accumulation and three genotypes were heterozygous/heterogenous. All three markers classified the soybean genotypes in the same manner but KASP marker is more efficient in marker-assisted selection/breeding for Cda1. This study offers valuable information to breeders and other researches regarding the selection of soybean germplasm with low cadmium accumulation in the pursuit of reducing the Cd-accumulation and assuring the food safety worldwide.

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Section: Resultsmentioning

confidence: 99%

Section: Dna Amplificationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Screening Soybean Germplasm for Presence of Cda1 Allele Involved in Low Cadmium Accumulation Using Molecular Markers

Ciucă¹,

Cristina²,

Petcu³

et al. 2023

RAR

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Identification of Candidate Genes for Soybean Storability via GWAS and WGCNA Approaches

Wu,

Wang,

Xie

et al. 2024

Agronomy

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Soybean (Glycine max (L.) Merr.) is an important crop for both food and feed, playing a significant role in agricultural production and the human diet. During long-term storage, soybean seeds often exhibit reduced quality, decreased germination, and lower seedling vigor, ultimately leading to significant yield reductions in soybean crops. Seed storage tolerance is a complex quantitative trait controlled by multiple genes and is also influenced by environmental factors during seed formation, harvest, and storage. This study aimed to evaluate soybean germplasms for their storage tolerance, identify quantitative trait nucleotides (QTNs) associated with seed storage tolerance traits, and screen for candidate genes. The storage tolerance of 168 soybean germplasms was evaluated, and 23,156 high-quality single nucleotide polymorphism (SNP) markers were screened and analyzed through a genome-wide association study (GWAS). Ultimately, 14 QTNs were identified as being associated with seed storage tolerance and were distributed across the eight chromosomes of soybean, with five QTNs (rs25887810, rs27941858, rs33981296, rs44713950, and rs18610980) being newly reported loci in this study. In the linkage disequilibrium regions of these SNPs, 256 genes were identified. By combining GWAS and weighted gene co-expression network analysis (WGCNA), eight hub genes (Glyma.03G058300, Glyma.04G1921100, Glyma.04G192600, Glyma.04G192900, Glyma.07G002000, Glyma.08G329400, Glyma.16G074600, Glyma.16G091400) were jointly identified. Through the analysis of expression patterns, two candidate genes (Glyma.03G058300, Glyma.16G074600) potentially involved in seed storage tolerance were ultimately identified. Additionally, haplotype analysis revealed that natural variations in Glyma.03G058300 could affect seed storage tolerance. The findings of this research provide a theoretical foundation for understanding the regulatory mechanism underlying soybean storage.

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Genome-Wide Association Study and Marker Development for Fusarium Oxysporum Root Rot Resistance in Soybean

Wang,

Han,

Meng

et al. 2024

IJMS

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Fusarium oxysporum root rot (FORR) is an important disease threatening soybean production. The development of marker-assisted selection (MAS) molecular markers will help accelerate the disease resistance breeding process and achieve the breeding goal of improving soybean disease resistance. This study evaluated the FORR disease resistance of 356 soybean germplasm accessions (SGAs) and screened resistance-related loci using genome-wide association analysis (GWAS) to develop molecular markers for MAS. A total of 1,355,930 high-quality SNPs were analyzed, 150 SNP sites significantly associated with FORR resistance were identified, and these sites were distributed within 41 QTLs. Additionally, 240 candidate genes were screened near these QTL regions, involving multiple functions such as hormone metabolism, signal transduction, stress defense, and growth regulation. Cleaved amplified polymorphic sequence (CAPS) and Kompetitive Allele-Specific PCR (KASP) molecular markers were developed based on candidate genes with significant SNP loci and beneficial haplotypes. The CAPS markers, S15_50486939-CAPS1 and S15_50452626-CAPS2, can effectively distinguish resistant and sensitive genotypes through enzyme digestion. The KASP marker is based on S07_19078765-G/T and exhibits a genotype clustering pattern consistent with disease resistance, demonstrating its application value in breeding. The CAPS and KASP markers developed in this study can provide reliable tools for MAS in FORR disease-resistant varieties. The research results will help reveal the genetic structure of FORR disease resistance and provide support for efficient breeding.

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Novel QTL for Low Seed Cadmium Accumulation in Soybean

Cited by 3 publications

References 47 publications

Screening Soybean Germplasm for Presence of Cda1 Allele Involved in Low Cadmium Accumulation Using Molecular Markers

Screening Soybean Germplasm for Presence of Cda1 Allele Involved in Low Cadmium Accumulation Using Molecular Markers

Identification of Candidate Genes for Soybean Storability via GWAS and WGCNA Approaches

Genome-Wide Association Study and Marker Development for Fusarium Oxysporum Root Rot Resistance in Soybean

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