Allelic Variation and Distribution of the Major Maturity Genes in Different Soybean Collections

Miladinović, Jegor; Ćeran, Marina; Đorđević, Vuk; Balešević-Tubić, Svetlana; Petrović, Kristina; Đukić, Vojin; Miladinović, Dragana

doi:10.3389/fpls.2018.01286

Cited by 30 publications

(35 citation statements)

References 52 publications

(77 reference statements)

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“…One of those loci harbored the SNP Chr10_45903960. Two of the SNPs associated with maturity, Chr10_45903960 and Chr20_41339091, were located into the E2 and E4 loci that have been reported to control maturity in soybean [10]. For the plant height-related SNPs, previous investigations showed discrepancy in terms of SNP location.…”

Section: Discussionmentioning

confidence: 93%

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Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Ravelombola¹,

Qin²,

Shi³

et al. 2020

Preprint

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BackgroundSoybean [Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy.Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). Population structure was inferred using STRUCTURE 2.3.4, GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that: a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci (E2, E4, and Dt1) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900, Glyma.19g200800, Glyma.09g196700, and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP (if no annotated genes found close the top one) for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent.Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits in soybean through marker-assisted selection (MAS) and GS in breeding programs. After validation, the candidate genes can be transferred to new cultivars using the linked SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

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Section: Discussionmentioning

confidence: 93%

“…Candidate genes such as Glyma11g14150, Glyma16g02840, and Glyma16g03580 have been suggested to control maturity in soybean [8]. The most described loci affecting maturity in soybean are E1-E10 and J [10].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Ravelombola¹,

Qin²,

Shi³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…One of those loci harbored the SNP Chr10_45903960. Two of the SNPs associated with maturity, Chr10_45903960 and Chr20_41339091, were located into the E2 and E4 loci that have been reported to control maturity in soybean (Miladinović et al, 2018). For the plant height-related SNPs, previous investigations showed discrepancy in terms of SNP location.…”

Section: Discussionmentioning

confidence: 93%

“…Candidate genes such as Glyma11g14150, Glyma16g02840, and Glyma16g03580 have been suggested to control maturity in soybean (Zhang et al 2015a). The most described loci affecting maturity in soybean are E1-E10 and J (Miladinović et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Ravelombola

Qin²,

Shi

et al. 2019

Preprint

View full text Add to dashboard Cite

Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

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“…Since soybean production is highly sensitive to photoperiod, efforts have been spent on studying the flowering and maturation time of soybean to maintain the yield at different latitudes. E1-E4 are the well-characterized major loci controlling the flowering and maturation times of soybean (Jiang et al 2014;Miladinovic et al 2018;Tsubokura et al 2014). In a recent study, using two genetic populations with fixed genotypes in the E1-E4 loci, researchers were able to identify two other loci in soybean contributing to flowering and maturation, specifically in chromosome 4 of the Dongnong 50 × Wm82 RIL population and in chromosome 6 of the Suinong 14 × Enrei RIL population, respectively (Kong et al 2018).…”

Section: Progress On Soybean Molecular Breeding In Chinamentioning

confidence: 99%

Impacts of genomic research on soybean improvement in East Asia

Wang

Jiang

et al. 2019

Theor Appl Genet

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It has been commonly accepted that soybean domestication originated in East Asia. Although East Asia has the historical merit in soybean production, the USA has become the top soybean producer in the world since 1950s. Following that, Brazil and Argentina have been the major soybean producers since 1970s and 1990s, respectively. China has once been the exporter of soybean to Japan before 1990s, yet she became a net soybean importer as Japan and the Republic of Korea do. Furthermore, the soybean yield per unit area in East Asia has stagnated during the past decade. To improve soybean production and enhance food security in these East Asian countries, much investment has been made, especially in the breeding of better performing soybean germplasms. As a result, China, Japan, and the Republic of Korea have become three important centers for soybean genomic research. With new technologies, the rate and precision of the identification of important genomic loci associated with desired traits from germplasm collections or mutants have increased significantly. Genome editing on soybean is also becoming more established. The year 2019 marked a new era for crop genome editing in the commercialization of the first genome-edited plant product, which is a high-oleic-acid soybean oil. In this review, we have summarized the latest developments in soybean breeding technologies and the remarkable progress in soybean breeding-related research in China, Japan, and the Republic of Korea. Communicated by Rajeev K. Varshney.

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Allelic Variation and Distribution of the Major Maturity Genes in Different Soybean Collections

Cited by 30 publications

References 52 publications

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Impacts of genomic research on soybean improvement in East Asia

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