Genetic dynamics of earlier maturity group emergence in south-to-north extension of Northeast China soybeans

Fu, Mengmeng; Wang, Yanping; Haixiang, Ren; Weiguang, Du; Wang, DeLiang; Rongjun, Bao; Yang, Xianlin; Zhang, Tian; Fu, Lixin; Cheng, Yongqiang; JiangShun, Su; Sun, Bincheng; Zhao, Jinming; Gai, Junyi

doi:10.1007/s00122-020-03558-4

Cited by 17 publications

(29 citation statements)

References 55 publications

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“…For example, there were a total of 261 alleles on 75 loci in Chinese cultivated soybeans for drought tolerance, and 46 alleles (17.6%) on 27 loci (36.0%) were changed in RC relative to LR (Wang et al, 2020). In addition, there were a total of 342 alleles on 81 loci in Northeast China soybeans for earliness, and 143 alleles (41.8%) on 67 loci (82.7%) were changed in the early group relative to the late group (Fu et al, 2020). The predicted NDVI of progenies in the optimal crosses among the 341 lines based on the linkage model.…”

Section: Qtl-allele Matrices Of Ndvi and Chl And Their Evolution Frommentioning

confidence: 98%

“…The 341 soybean accessions were genotyped with RAD-seq (restriction site-associated DNA sequencing) in previous studies (He et al, 2017;Fu et al, 2020;Liu et al, 2020). A total of 145,558, 82,966, and 98,482 SNPs were recovered in these three studies, respectively, and the intersection of SNP data from different studies was taken and filtered with a minor allele frequency > 2% (each allele is present in at least six individuals).…”

Section: Snp Genotyping and Snpldb Assemblymentioning

confidence: 99%

“…Both phenotypic and genotypic analysis showed that the two spectral reflectance traits were genetically conservative in comparison to the agronomic traits, such as seed yield, 100 seed weight, days to flowering (He et al, 2017;Zhang et al, 2019;Fu et al, 2020). Because in the present results, (i) no significant phenotypic improvements were observed in RC, and trait values were low in LR and RC; (ii) there was a limited number of alleles per locus; (iii) there was a large number of shared wild alleles among WA, LR, and RC, few new alleles, and little exclusion of wild alleles; and (iv) the recombination potential was low.…”

Section: Genetic Conservativeness Of Ndvi and Chl Their Improvement mentioning

confidence: 99%

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Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population

et al. 2021

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The QTL-allele system underlying two spectral reflectance physiological traits, NDVI (normalized difference vegetation index) and CHL (chlorophyll index), related to plant growth and yield was studied in the Chinese soybean germplasm population (CSGP), which consisted of 341 wild accessions (WA), farmer landraces (LR), and released cultivars (RC). Samples were evaluated in the Photosynthetic System II imaging platform at Nanjing Agricultural University. The NDVI and CHL data were obtained from hyperspectral reflectance images in a randomized incomplete block design experiment with two replicates. The NDVI and CHL ranged from 0.05–0.18 and 1.20–4.78, had averages of 0.11 and 3.57, and had heritabilities of 78.3% and 69.2%, respectively; the values of NDVI and CHL were both significantly higher in LR and RC than in WA. Using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) method, 38 and 32 QTLs with 89 and 82 alleles and 2–4 and 2–6 alleles per locus were identified for NDVI and CHL, respectively, which explained 48.36% and 51.35% of the phenotypic variation for NDVI and CHL, respectively. The QTL-allele matrices were established and separated into WA, LR, and RC submatrices. From WA to LR + RC, 4 alleles and 2 new loci emerged, and 1 allele was excluded for NDVI, whereas 6 alleles emerged, and no alleles were excluded, in LR + RC for CHL. Recombination was the major motivation of evolutionary differences. For NDVI and CHL, 39 and 32 candidate genes were annotated and assigned to GO groups, respectively, indicating a complex gene network. The NDVI and CHL were upstream traits that were relatively conservative in their genetic changes compared with those of downstream agronomic traits. High-throughput phenotyping integrated with RTM-GWAS provides an efficient procedure for studying the population genetics of traits.

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Section: Qtl-allele Matrices Of Ndvi and Chl And Their Evolution Frommentioning

confidence: 98%

Section: Snp Genotyping and Snpldb Assemblymentioning

confidence: 99%

Section: Genetic Conservativeness Of Ndvi and Chl Their Improvement mentioning

confidence: 99%

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Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population

et al. 2021

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“…Using RTM‐GWAS to analyze genetic changes in DTF values at the population level from south to north in Northeast China, Fu et al. (2020a) reported its genetic dynamics including allele inheritance or migration, new allele emergence or mutation, old allele exclusion or selection against them, and allele recombination (Fu et al., 2020a). Liu et al.…”

Section: Introductionmentioning

confidence: 99%

Growth period QTL‐allele constitution of global soybeans and its differential evolution changes in geographic adaptation versus maturity group extension

Liu

Cao³

et al. 2021

The Plant Journal

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Summary Soybean (Glycine max (L.) Merr.) has been disseminated globally as a photoperiod/temperature‐sensitive crop with extremely diverse days to flowering (DTF) and days to maturity (DTM) values. A population with 371 global varieties covering 13 geographic regions and 13 maturity groups (MGs) was analyzed for its DTF and DTM QTL‐allele constitution using restricted two‐stage multi‐locus genome‐wide association study (RTM‐GWAS). Genotypes with 20 701 genome‐wide SNPLDBs (single‐nucleotide polymorphism linkage disequilibrium blocks) containing 55 404 haplotypes were observed, and 52 DTF QTLs and 59 DTM QTLs (including 29 and 21 new ones) with 241 and 246 alleles (two to 13 per locus) were detected, explaining 84.8% and 74.4% of the phenotypic variance, respectively. The QTL‐allele matrix characterized with all QTL‐allele information of each variety in the global population was established and subsequently separated into geographic and MG set submatrices. Direct comparisons among them revealed that the genetic adaptation from the origin to geographic subpopulations was characterized by new allele/new locus emergence (mutation) but little allele exclusion (selection), while that from the primary MG set to emerged early and late MG sets was characterized by allele exclusion without allele emergence. The evolutionary changes involved mainly 72 DTF and 71 DTM alleles on 28 respective loci, 10–12 loci each with three to six alleles being most active. Further recombination potential for faster maturation (12–21 days) or slower maturation (14–56 days) supported allele convergence (recombination) as a constant genetic factor in addition to migration (inheritance). From the QTLs, 44 DTF and 36 DTM candidate genes were annotated and grouped respectively into nine biological processes, indicating multi‐functional DTF/DTM genes are involved in a complex gene network. In summary, we identified QTL‐alleles relatively thoroughly using RTM‐GWAS for direct matrix comparisons and subsequent analysis.

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“…Twelve maturity loci – E1 - E11 and J – have been proposed, and some have been identified [ 20 ]. Recently, Fu et al [ 21 ] proposed some yet-unmapped maturity QTLs related to the south-to-north extension of Northeast China soybean. Notably, most known maturity loci are homologs of circadian clock genes.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

Yue

Sapey

et al. 2021

BMC Genomics

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Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

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Genetic dynamics of earlier maturity group emergence in south-to-north extension of Northeast China soybeans

Cited by 17 publications

References 55 publications

Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population

Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population

Growth period QTL‐allele constitution of global soybeans and its differential evolution changes in geographic adaptation versus maturity group extension

Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

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