Detecting the QTL-allele system controlling seed-flooding tolerance in a nested association mapping population of soybean

Ali, Muhammad Jaffer; Xing, Guangnan; He, Jianbo; Zhao, Tuanjie; Gai, Junyi

doi:10.1016/j.cj.2020.06.008

Cited by 20 publications

(6 citation statements)

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“…GWAS has identified 26 main effect QTL with 63 alleles. The best genotype was predicted to have a value of 1.924, and 33 candidate genes were identified for six biological processes (Ali et al, 2020). Wu et al (2020) evaluated a panel of 320 soybean plant introductions (PIs) for flooding tolerance.…”

Section: Gwas-based Identified Qtl and Genes For Flood Tolerancementioning

confidence: 99%

The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean – An review

et al. 2022

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Abiotic stresses and climate changes cause severe loss of yield and quality of crops and reduce the production area worldwide. Flooding stress curtails soybean growth, yield, and quality and ultimately threatens the global food supply chain. Flooding tolerance is a multigenic trait. Tremendous research in molecular breeding explored the potential genomic regions governing flood tolerance in soybean. The most robust way to develop flooding tolerance in soybean is by using molecular methods, including quantitative trait loci (QTL) mapping, identification of transcriptomes, transcription factor analysis, CRISPR/Cas9, and to some extent, genome-wide association studies (GWAS), and multi-omics techniques. These powerful molecular tools have deepened our knowledge about the molecular mechanism of flooding stress tolerance. Besides all this, using conventional breeding methods (hybridization, introduction, and backcrossing) and other agronomic practices is also helpful in combating the rising flooding threats to the soybean crop. The current review aims to summarize recent advancements in breeding flood-tolerant soybean, mainly by using molecular and conventional tools and their prospects. This updated picture will be a treasure trove for future researchers to comprehend the foundation of flooding tolerance in soybean and cover the given research gaps to develop tolerant soybean cultivars able to sustain growth under extreme climatic changes.

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Section: Gwas-based Identified Qtl and Genes For Flood Tolerancementioning

confidence: 99%

The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean – An review

et al. 2022

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“…Besides the QTL hotspots detected on Chromosome 6 and Chromosome 8, we also identified some QTLs on other chromosomes, including Chromosome 1, Chromosome 3, Chromosome 15, and so on. By comparing the genomic position of these QTLs with the previously identified loci, qGR-1-1 and qEC-1-1 are overlapped with the Flood tolerance 6-1 locus coded on the SoyBase website detected by Rizal and Karki [ 54 ], and the region of qEC-17-1 on Chromosome 17 also includes QTL SFT_17-52 and RSL-a-17-1a found by Dhungana et al [ 16 ] and Ali et al [ 21 ].…”

Section: Discussionmentioning

confidence: 92%

“…Moreover, all the favorable positive alleles of identified QTLs were derived from PI342616B, which supported the view that wild soybean gene pool is an abundant source of elite stress-tolerant genes. Wild soybean, as the progenitor of cultivated soybean, has been reported to display high contents of oil and protein, rich in genetic diversity, strong adaptability, and tolerance to various stresses [ 21 , 22 , 23 ]. Due to the favorable tolerance alleles contributed by wild soybean, it has become an efficient way to improve the seed-flooding tolerance of elite soybean varieties by introducing the seed-flooding tolerant QTLs/genes from wild soybean into elite cultivars.…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, this QTL was near I genetic locus which controls the seed coat pigmentation [ 20 ]. A total of 33 QTLs including 26 main-effect ones for the seed-flooding tolerance parameter of relative seedling length were identified in two related RIL populations with a common tolerance parent M8206 by using a restricted two-stage multi-locus multi-allele genome-wide association study [ 21 ]. By using a genome-wide association analysis (GWAS) method, 14 SNPs were found to be associated with the tolerance to waterlogging [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

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Genetic Dissection of Extreme Seed-Flooding Tolerance in a Wild Soybean PI342618B by Linkage Mapping and Candidate Gene Analysis

Sharmin

et al. 2023

Plants

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Seed-flooding stress is one of major abiotic constraints that adversely affects soybean production worldwide. Identifying tolerant germplasms and revealing the genetic basis of seed-flooding tolerance are imperative goals for soybean breeding. In the present study, high-density linkage maps of two inter-specific recombinant inbred line (RIL) populations, named NJIRNP and NJIR4P, were utilized to identify major quantitative trait loci (QTLs) for seed-flooding tolerance using three parameters viz., germination rate (GR), normal seedling rate (NSR), and electrical conductivity (EC). A total of 25 and 18 QTLs were detected by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively, and 12 common QTLs were identified through both methods. All favorable alleles for the tolerance are notably from the wild soybean parent. Moreover, four digenic epistatic QTL pairs were identified, and three of them showed no main effects. In addition, the pigmented soybean genotypes exhibited high seed-flooding tolerance compared with yellow seed coat genotypes in both populations. Moreover, out of five identified QTLs, one major region containing multiple QTLs associated with all three traits was identified on Chromosome 8, and most of the QTLs within this hotspot were major loci (R2 > 10) and detectable in both populations and multiple environments. Based on the gene expression and functional annotation information, 10 candidate genes from QTL “hotspot 8-2” were screened for further analysis. Furthermore, the results of qRT-PCR and sequence analysis revealed that only one gene, GmDREB2 (Glyma.08G137600), was significantly induced under flooding stress and displayed a TTC tribasic insertion mutation of the nucleotide sequence in the tolerant wild parent (PI342618B). GmDREB2 encodes an ERF transcription factor, and the subcellular localization analysis using green fluorescent protein (GFP) revealed that GmDREB2 protein was localized in the nucleus and plasma membrane. Furthermore, overexpression of GmDREB2 significantly promoted the growth of soybean hairy roots, which might indicate its critical role in seed-flooding stress. Thus, GmDREB2 was considered as the most possible candidate gene for seed-flooding tolerance.

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“…The Bauer laboratory in Europe then constructed two sets of European-NAM (EU-NAM) populations using European Dent and Flint maize germplasms to analyze the genetic basis of maize [ 22 ]. Due to their powerful function in dissecting the genetic architecture of complex traits, NAM populations have been widely applied in various crops such as rice, wheat, barley, rapeseed, soybean, and peanut [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. The above studies have fully utilized the advantages of NAM populations, including abundant recombination between parents and families, and large genetic differences, which to some extent eliminated the negative effects of population structure.…”

Section: Introductionmentioning

confidence: 99%

Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize

Jiang

Liu

et al. 2023

Genes

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Ear diameter (ED) is a critical component of grain yield (GY) in maize (Zea mays L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map the ED-related quantitative trait locus (QTL) and SNPs associated with ED; and (2) identify putative functional genes that may affect ED in maize. To accomplish this, an elite maize inbred line, Ye107, which belongs to the Reid heterotic group, was used as a common parent and crossed with seven elite inbred lines from three different heterotic groups (Suwan1, Reid, and nonReid) that exhibited abundant genetic variation in ED. This led to the construction of a multi-parent population consisting of 1215 F7 recombinant inbred lines (F7RILs). A genome-wide association study (GWAS) and linkage analysis were then conducted for the multi-parent population using 264,694 high-quality SNPs generated via the genotyping-by-sequencing method. Our study identified a total of 11 SNPs that were significantly associated with ED through the GWAS, and three QTLs were revealed by the linkage analysis for ED. The major QTL on chromosome 1 was co-identified in the region by the GWAS at SNP_143985532. SNP_143985532, located upstream of the Zm00001d030559 gene, encodes a callose synthase that is expressed in various tissues, with the highest expression level in the maize ear primordium. Haplotype analysis indicated that the haplotype B (allele AA) of Zm00001d030559 was positively correlated with ED. The candidate genes and SNPs identified in this study provide crucial insights for future studies on the genetic mechanism of maize ED formation, cloning of ED-related genes, and genetic improvement of ED. These results may help develop important genetic resources for enhancing maize yield through marker-assisted breeding.

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Detecting the QTL-allele system controlling seed-flooding tolerance in a nested association mapping population of soybean

Cited by 20 publications

References 48 publications

The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean – An review

The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean – An review

Genetic Dissection of Extreme Seed-Flooding Tolerance in a Wild Soybean PI342618B by Linkage Mapping and Candidate Gene Analysis

Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize

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