scholarly journals The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Na Zhao ◽  
Xiaoyang Ding ◽  
Taotao Lian ◽  
Meng Wang ◽  
Yan Tong ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Glycine Soja ◽  
Wild Soybean ◽  
F1 Hybrids ◽  
Substantial Contribution ◽  
Duplicated Genes ◽  
Regulatory Changes ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Cultivated Soybean

Regulatory changes include divergence in both cis-elements and trans-factors, which play roles in organismal evolution. Whole genome duplications (WGD) followed by diploidization are a recurrent feature in the evolutionary history of angiosperms. Prior studies have shown that duplicated genes have different evolutionary fates due to variable selection constraints and results in genomic compositions with hallmarks of paleopolyploidy. The recent sequential WGDs and post-WGD evolution in the common ancestor of cultivated soybean (Glycine max) and wild soybean (Glycine soja), together with other models of gene duplication, have resulted in a highly duplicated genome. In this study, we investigated the transcriptional changes in G. soja and G. max. We identified a sizable proportion of interspecific differentially expressed genes (DEGs) and found parental expression level dominance of G. max in their F1 hybrids. By classifying genes into different regulatory divergence types, we found the trans-regulatory changes played a predominant role in transcriptional divergence between wild and cultivated soybean. The same gene ontology (GO) and protein family (Pfam) terms were found to be over-represented in DEGs and genes of cis-only between JY47 and GS, suggesting the substantial contribution of cis-regulatory divergences to the evolution of wild and cultivated soybeans. By further dissecting genes into five different duplication modes, we found genes in different duplication modes tend to accumulate different types of regulatory differences. A relatively higher proportion of cis-only regulatory divergences was detected in singleton, dispersed, proximal, and tandem duplicates than WGD duplicates and genome-wide level, which is in line with the prediction of gene balance hypothesis for the differential fates of duplicated genes post-WGD. The numbers of cis-only and trans-only regulated genes were similar for singletons, whereas there were more genes of trans-only than cis-only in the rest duplication types, especially in WGD in which there were two times more trans-only genes than that in cis-only type. Tandem duplicates showed the highest proportion of trans-only genes probably due to some special features of this class. In summary, our results demonstrate that genes in different duplication modes have different fates in transcriptional evolution underpinned by cis- or trans-regulatory divergences in soybean and likely in other paleopolyploid higher organisms.

scholarly journals Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution

2020 ◽  
Author(s):  
Akihiro Ezoe ◽  
Kazumasa Shirai ◽  
Kousuke Hanada
Keyword(s):  
Gene Duplication ◽  
Related Species ◽  
Plant Evolution ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Closely Related Species ◽  
Whole Genome Duplications ◽  
New Genes ◽  
Genome Duplications ◽  
Tandem Duplications

Abstract Gene duplication is a major mechanism to create new genes. After gene duplication, some duplicated genes undergo functionalization, whereas others largely maintain redundant functions. Duplicated genes comprise various degrees of functional diversification in plants. However, the evolutionary fate of high and low diversified duplicates is unclear at genomic scale. To infer high and low diversified duplicates in Arabidopsis thaliana genome, we generated a prediction method for predicting whether a pair of duplicate genes was subjected to high or low diversification based on the phenotypes of knock-out mutants. Among 4,017 pairs of recently duplicated A. thaliana genes, 1,052 and 600 are high and low diversified duplicate pairs, respectively. The predictions were validated based on the phenotypes of generated knock-down transgenic plants. We determined that the high diversified duplicates resulting from tandem duplications tend to have lineage-specific functions, whereas the low diversified duplicates produced by whole-genome duplications are related to essential signaling pathways. To assess the evolutionary impact of high and low diversified duplicates in closely related species, we compared the retention rates and selection pressures on the orthologs of A. thaliana duplicates in two closely related species. Interestingly, high diversified duplicates resulting from tandem duplications tend to be retained in multiple lineages under positive selection. Low diversified duplicates by whole-genome duplications tend to be retained in multiple lineages under purifying selection. Taken together, the functional diversities determined by different duplication mechanisms had distinct effects on plant evolution.

scholarly journals Genetic Control and Geo-Climate Adaptation of Pod Dehiscence Provide Novel Insights into Soybean Domestication

2019 ◽  
Vol 10 (2) ◽  
pp. 545-554 ◽  
Author(s):  
Jiaoping Zhang ◽  
Asheesh K. Singh
Keyword(s):  
Association Analysis ◽  
Climate Adaptation ◽  
Southern China ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Candidate Gene Association ◽  
Genome Wide ◽  
Cultivated Soybean ◽  
Soybean Domestication ◽  
Pod Dehiscence

Loss of pod dehiscence was a key step in soybean [Glycine max (L.) Merr.] domestication. Genome-wide association analysis for soybean shattering identified loci harboring Pdh1, NST1A and SHAT1-5. Pairwise epistatic interactions were observed, and the dehiscent Pdh1 overcomes resistance conferred by NST1A or SHAT1-5 locus. Further candidate gene association analysis identified a nonsense mutation in NST1A associated with pod dehiscence. Geographic analysis showed that in Northeast China (NEC), indehiscence at both Pdh1 and NST1A were required in cultivated soybean, while indehiscent Pdh1 alone is capable of preventing shattering in Huang-Huai-Hai (HHH) valleys. Indehiscent Pdh1 allele was only identified in wild soybean (Glycine soja L.) accession from HHH valleys suggesting that it may have originated in this region. No specific indehiscence was required in Southern China. Geo-climatic investigation revealed strong correlation between relative humidity and frequency of indehiscent Pdh1 across China. This study demonstrates that epistatic interaction between Pdh1 and NST1A fulfills a pivotal role in determining the level of resistance against pod dehiscence, and humidity shapes the distribution of indehiscent alleles. Our results give further evidence to the hypothesis that HHH valleys was at least one of the origin centers of cultivated soybean.

Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 715-723 ◽  
Author(s):  
P. J. Maughan ◽  
M. A. Saghai Maroof ◽  
G. R. Buss
Keyword(s):  
Genetic Markers ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Allelic Diversity ◽  
Sequence Length ◽  
Length Polymorphisms ◽  
Ssr Loci ◽  
Low Levels ◽  
Cultivated Soybean ◽  
Simple Sequence

The objectives of this study were to (i) assess the extent of genetic variation in soybean microsatellites (simple sequence repeats or SSRs), (ii) assay for amplified sequence length polymorphisms (ASLPs), and (iii) evaluate the usefulness of SSRs and ASLPs as genetic markers. Five microsatellites detected a total of 79 variants (alleles) in a sample of 94 accessions of wild (Glycine soja) and cultivated soybean (G. max). F2 segregation analysis of four of the five microsatellites identified these variants (alleles) with four loci located in independent linkage groups. The number of alleles per microsatellite locus ranged from 5 to 21; to our knowledge these are the largest numbers of alleles for single Mendelian loci reported in soybean. Allelic diversity for the SSR loci was greater in wild than in cultivated soybean. Overall, 43 more SSR alleles were detected in wild than in cultivated soybean. These results indicate that SSRs are the marker of choice, especially for species with low levels of variation as detected by other types of markers. Two alleles were detected at each of the three ASLP loci examined. A total of six ASLP alleles were observed in cultivated soybean and five were observed in wild soybean; all alleles detected in wild soybean were present in cultivated soybean. Allelic diversity values for the ASLP loci were near previous estimates for restriction fragment length polymorphisms and therefore ASLPs may be useful as genetic markers in site-directed mapping.Key words: microsatellite, simple sequence repeat, soybean, amplified sequence length polymorphism, genetic mapping.

Conservation of leghemoglobin heterogeneity and structures in cultivated and wild soybean

1985 ◽  
Vol 63 (11) ◽  
pp. 1951-1956 ◽  
Author(s):  
W. H. Fuchsman ◽  
R. G. Palmer
Keyword(s):  
Glycine Max ◽  
Isoelectric Focusing ◽  
Bradyrhizobium Japonicum ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Rhizobium Japonicum ◽  
Plant Introductions ◽  
Glycine Max L ◽  
Cultivated Soybean ◽  
Selection Of

The leghemoglobins from a genetically diverse selection of 69 cultivated soybean (Glycine max (L.) Merr.) cultivars and plant introductions and 18 wild soybean (Glycine soja Sieb. & Zucc.) plant introductions all consist of the same set of major leghemoglobins (a, c1, c2, c3), as determined by analytical isoelectric focusing. The conservation of both leghemoglobin heterogeneity and also all four major leghemoglobin structures provides strong circumstantial evidence that leghemoglobin heterogeneity is functional. Glycine max and G. soja produced the same leghemoglobins in the presence of Bradyrhizobium japonicum (Kirchner) Jordan and in the presence of fast-growing Rhizobium japonicum.

scholarly journals Comparative Ecophysiological Study of Salt Stress for Wild and Cultivated Soybean Species from the Yellow River Delta, China

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Gang Wu ◽  
Zhengda Zhou ◽  
Peng Chen ◽  
Xiaoli Tang ◽  
Hongbo Shao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Yellow River ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Yellow River Delta ◽  
Salt Resistance ◽  
Nacl Concentration ◽  
Relative Water ◽  
Cultivated Soybean ◽  
Almost All

Osmotic and ionic stresses were the primary and instant damage produced by salt stress. They can also bring about other secondary stresses. Soybean is an important economic crop and the wild soybean aroused increasing attention for its excellent performance in salt resistance. For this reason, we compared the different performances ofGlycine maxL. (ZH13) andGlycine sojaL. (BB52) in both young and mature seedlings, hoping to clarify the specific reasons. Our research revealed that, compared to the cultivated soybean, the wild soybean was able to maintain higher water potential and relative water content (RWC), accumulate more amount of proline and glycine betaine, reduce the contents of Na+and Cl−by faster efflux, and cut down the efflux of the K+as well as keep higher K+/Na+ratio. And what is more is that, almost all the excel behaviors became particularly obvious under higher NaCl concentration (300 mM). Therefore, according to all the detections and comparisons, we concluded that the wild soybean had different tolerance mechanisms and better salt resistance. It should be used as eminent germplasm resource to enhance the resistant ability of cultivated soybean or even other crops.

scholarly journals Nutrient reabsorption mechanism adapted to low phosphorus in wild and cultivated soybean varieties

2020 ◽  
Author(s):  
wenyue shen ◽  
Rui Guo ◽  
yaxuan zhao ◽  
danping liu ◽  
jing chen ◽  
...  
Keyword(s):  
Glycine Soja ◽  
Tricarboxylic Acid Cycle ◽  
Wild Soybean ◽  
P Deficiency ◽  
Nitrogenous Compounds ◽  
Hexose Phosphate ◽  
Low Phosphorus ◽  
Young Leaves ◽  
Essential Nutrient ◽  
Cultivated Soybean

Phosphorus (P) is an essential nutrient element for plants. Wild soybean (Glycine soja) expresses higher tolerance to P-limited environment compared to cultivated soybeans (Glycine max). In this study, the response of ionomics and metabonomics in young and old leaves of two soybean varieties under low P were studied. Our results showed that the tolerance of low P in wild soybean can be improved by promoting the accumulation of Mg2+, Fe3+, and SO42- in young and old leaves and the transportation of NO3− and H2PO4− from old to young leaves. The young and old leaves of wild soybean under low P accumulated sugars including maltose and sucrose, amino acids including asparagine and glutamine, and nitrogenous compounds including tyramine, and enhanced the tricarboxylic acid cycle metabolism, especially in young leaves, but decreased the content of hexose-phosphate metabolites. Our experiment indicated that wild soybean can tolerate low P by enhancing the energy metabolism in young and old leaves, promoting the transportation and reuse of sugars and amino acid metabolites from old to young leaves, and mobilizing Pi from hexose-phosphate of old leaves to young leaves. Our results provide a new insight for the cultivation of new soybean varieties with tolerance to P deficiency.

Genetic diversity and population structure of wild soybean (Glycine soja Sieb. and Zucc.) accessions in Korea

2014 ◽  
Vol 12 (S1) ◽  
pp. S45-S48 ◽  
Author(s):  
Kil Hyun Kim ◽  
Seukki Lee ◽  
Min-Jung Seo ◽  
Gi-An Lee ◽  
Kyung-Ho Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Glycine Soja ◽  
Crop Improvement ◽  
Wild Soybean ◽  
Background Information ◽  
Ssr Loci ◽  
Breeding Programmes ◽  
Western Side ◽  
Cultivated Soybean

Genetic variation in wild soybean (Glycine soja Sieb. and Zucc.) is a valuable resource for crop improvement efforts. Soybean is believed to have originated from China, Korea, and Japan, but little is known about the diversity or evolution of Korean wild soybean. Therefore, in this study, we evaluated the genetic diversity and population structure of 733 G. soja accessions collected in Korea using 21 simple sequence repeat (SSR) markers. The SSR loci produced 539 alleles (25.7 per locus) with a mean genetic diversity of 0.882 in these accessions. Rare alleles, those with a frequency of less than 5%, represented 75% of the total number. This collection was divided into two populations based on the principal coordinate analysis. Accessions from population 1 were distributed throughout the country, whereas most of the accessions from population 2 were distributed on the western side of the Taebaek and Sobaek mountains. The Korean G. soja collection evaluated in this study should provide useful background information for allele mining approach and breeding programmes to introgress alleles into the cultivated soybean (G. max (L). Merr.) from wild soybean.

DNA methylation polymorphism in annual wild soybean (Glycine soja Sieb. et Zucc.) and cultivated soybean (G. max L. Merr.)

2009 ◽  
Vol 89 (5) ◽  
pp. 851-863 ◽  
Author(s):  
X Zhong ◽  
Y Wang ◽  
X Liu ◽  
L Gong ◽  
Y Ma ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fragment Length Polymorphism ◽  
Epigenetic Modification ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Homology Search ◽  
Aflp Analysis ◽  
Functional Relevance ◽  
Cultivated Soybean ◽  
Human Selection

To study DNA methylation polymorphism in soybean, 20 and 27 lines of annual wild and cultivated soybeans, respectively, were selected from previously established “Soybean Core Collections in China”, and subjected to methylation-sensitive amplified polymorphism (MSAP) analysis. Twenty-seven primer pairs generated 984 CG/CNG methylation sites across the 47 lines, and the data were dissected into methylation-sensitive (MS) and methylation-insensitive(MIS) polymorphisms. The calculated MSP vs. MISP for wild soybeans were 34.65 vs. 34.76%, while corresponding results for the cultivated soybeans were 47.05 vs. 47.15%, indicating higher levels of MSP and MISP in cultivated than in wild soybeans. These results were incongruent with the amplified fragment length polymorphism (AFLP) analysis of the same soybean lines, and suggested enhanced DNA methylation polymorphism due to human selection. All three markers, MSP, MISP and AFLP, enabled clustering of the soybean lines into two distinct groups each predominantly containing wild or cultivated ones. Homology search indicated that 12 out of 24 sequenced MSPs had significant similarities to known-function or predicated genes, suggesting possible functional relevance of the methylation polymorphism. No significant association between MSP and MISP or MSP and AFLP was detected. Our results suggest that DNA methylation polymorphism in soybean has been under both natural and human selections, implicating possible roles of this epigenetic modification in genome evolution and domestication.Key words: Annual wild soybean (Glycine soja), cultivated soybean (G. max), DNA methylation polymorphism, epigenetic variation, evolution, domestication

scholarly journals Novel resistance strategies to soybean cyst nematode (SCN) in wild soybean

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Janice Kofsky ◽  
Hengyou Zhang ◽  
Bao-Hua Song
Keyword(s):  
Gene Pool ◽  
Soybean Cyst Nematode ◽  
Agronomic Traits ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Cyst Nematode ◽  
Resistance Response ◽  
Soybean Cultivars ◽  
Scn Resistance ◽  
Cultivated Soybean

AbstractSoybean cyst nematode (SCN, Heterodera glycine Ichinohe) is the most damaging soybean pest worldwide and management of SCN remains challenging. The current SCN resistant soybean cultivars, mainly developed from the cultivated soybean gene pool, are losing resistance due to SCN race shifts. The domestication process and modern breeding practices of soybean cultivars often involve strong selection for desired agronomic traits, and thus, decreased genetic variation in modern cultivars, which consequently resulted in limited sources of SCN resistance. Wild soybean (Glycine soja) is the wild ancestor of cultivated soybean (Glycine max) and it’s gene pool is indisputably more diverse than G. max. Our aim is to identify novel resistant genetic resources from wild soybean for the development of new SCN resistant cultivars. In this study, resistance response to HG type 2.5.7 (race 5) of SCN was investigated in a newly identified SCN resistant ecotype, NRS100. To understand the resistance mechanism in this ecotype, we compared RNA seq-based transcriptomes of NRS100 with two SCN-susceptible accessions of G. soja and G. max, as well as an extensively studied SCN resistant cultivar, Peking, under both control and nematode J2-treated conditions. The proposed mechanisms of resistance in NRS100 includes the suppression of the jasmonic acid (JA) signaling pathway in order to allow for salicylic acid (SA) signaling-activated resistance response and polyamine synthesis to promote structural integrity of root cell walls. Our study identifies a set of novel candidate genes and associated pathways involved in SCN resistance and the finding provides insight into the mechanism of SCN resistance in wild soybean, advancing the understanding of resistance and the use of wild soybean-sourced resistance for soybean improvement.

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