scholarly journals Dissection of soybean populations according to selection signatures based on whole-genome sequences

GigaScience ◽  
2019 ◽  
Vol 8 (12) ◽  
Author(s):  
Jae-Yoon Kim ◽  
Seongmun Jeong ◽  
Kyoung Hyoun Kim ◽  
Won-Jun Lim ◽  
Ho-Yeon Lee ◽  
...  
Keyword(s):  
Seed Development ◽  
Soybean Cyst Nematode ◽  
Agronomic Traits ◽  
Cyst Nematode ◽  
Wild Type ◽  
Selection Signatures ◽  
Genetic Traits ◽  
Genome Wide ◽  
Core Set ◽  
Genomic Regions

Abstract Background Domestication and improvement processes, accompanied by selections and adaptations, have generated genome-wide divergence and stratification in soybean populations. Simultaneously, soybean populations, which comprise diverse subpopulations, have developed their own adaptive characteristics enhancing fitness, resistance, agronomic traits, and morphological features. The genetic traits underlying these characteristics play a fundamental role in improving other soybean populations. Results This study focused on identifying the selection signatures and adaptive characteristics in soybean populations. A core set of 245 accessions (112 wild-type, 79 landrace, and 54 improvement soybeans) selected from 4,234 soybean accessions was re-sequenced. Their genomic architectures were examined according to the domestication and improvement, and accessions were then classified into 3 wild-type, 2 landrace, and 2 improvement subgroups based on various population analyses. Selection and gene set enrichment analyses revealed that the landrace subgroups have selection signals for soybean-cyst nematode HG type 0 and seed development with germination, and that the improvement subgroups have selection signals for plant development with viability and seed development with embryo development, respectively. The adaptive characteristic for soybean-cyst nematode was partially underpinned by multiple resistance accessions, and the characteristics related to seed development were supported by our phenotypic findings for seed weights. Furthermore, their adaptive characteristics were also confirmed as genome-based evidence, and unique genomic regions that exhibit distinct selection and selective sweep patterns were revealed for 13 candidate genes. Conclusions Although our findings require further biological validation, they provide valuable information about soybean breeding strategies and present new options for breeders seeking donor lines to improve soybean populations.

scholarly journals Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax

2018 ◽  
Vol 19 (8) ◽  
pp. 2303 ◽  
Author(s):  
Frank You ◽  
Jin Xiao ◽  
Pingchuan Li ◽  
Zhen Yao ◽  
Gaofeng Jia ◽  
...  
Keyword(s):  
Association Study ◽  
Seed Yield ◽  
Phenotypic Variation ◽  
Genome Wide Association Study ◽  
Oil Quality ◽  
Genome Wide Association ◽  
Selection Signatures ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 quantitative trait loci (QTL) for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48–73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8–14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.

scholarly journals Genome-wide association study and genomic selection for soybean chlorophyll content associated with soybean cyst nematode tolerance

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Waltram Second Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Liana Nice ◽  
Yong Bao ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Candidate Genes ◽  
Chlorophyll Content ◽  
Soybean Cyst Nematode ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Cyst Nematode ◽  
Leaf Chlorophyll ◽  
Genome Wide ◽  
Soybean Leaf

Abstract Background Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production. In the United States alone, SCN damage accounted for more than $1 billion loss annually. With a narrow genetic background of the currently available SCN-resistant commercial cultivars, high risk of resistance breakdown can occur. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify QTL, SNP markers, and candidate genes associated with soybean leaf chlorophyll content tolerance to SCN infection, and to carry out a genomic selection (GS) study for the chlorophyll content tolerance. Results A total of 172 soybean genotypes were evaluated for the effect of SCN HG Type 1.2.3.5.6.7 (race 4) on soybean leaf chlorophyll. The soybean lines were genotyped using a total of 4089 filtered and high-quality SNPs. Results showed that (1) a large variation in SCN tolerance based on leaf chlorophyll content indices (CCI); (2) a total of 22, 14, and 16 SNPs associated with CCI of non-SCN-infected plants, SCN-infected plants, and reduction of CCI SCN, respectively; (3) a new locus of chlorophyll content tolerance to SCN mapped on chromosome 3; (4) candidate genes encoding for Leucine-rich repeat protein, plant hormone signaling molecules, and biomolecule transporters; and (5) an average GS accuracy ranging from 0.31 to 0.46 with all SNPs and varying from 0.55 to 0.76 when GWAS-derived SNP markers were used across five models. This study demonstrated the potential of using genome-wide selection to breed chlorophyll-content-tolerant soybean for managing SCN. Conclusions In this study, soybean accessions with higher CCI under SCN infestation, and molecular markers associated with chlorophyll content related to SCN were identified. In addition, a total of 15 candidate genes associated with chlorophyll content tolerance to SCN in soybean were also identified. These candidate genes will lead to a better understanding of the molecular mechanisms that control chlorophyll content tolerance to SCN in soybean. Genomic selection analysis of chlorophyll content tolerance to SCN showed that using significant SNPs obtained from GWAS could provide better GS accuracy.

scholarly journals Soybean Cyst Nematode Reduces Soybean Yield Without Causing Obvious Aboveground Symptoms

Plant Disease ◽  
2003 ◽  
Vol 87 (6) ◽  
pp. 623-628 ◽  
Author(s):  
J. Wang ◽  
T. L. Niblack ◽  
J. A. Tremain ◽  
W. J. Wiebold ◽  
G. L. Tylka ◽  
...  
Keyword(s):  
Seed Development ◽  
Soybean Cyst Nematode ◽  
Field Experiments ◽  
Heterodera Glycines ◽  
Biomass Accumulation ◽  
Cyst Nematode ◽  
Southern Illinois ◽  
Resistant Cultivars ◽  
Wide Range ◽  
Growth Development

Field experiments were conducted at locations in northern and southern Illinois, central Iowa, and central Missouri from 1997 to 1999 to investigate the effects of Heterodera glycines on soybean growth, development, and yield. A wide range of infestation levels was present at all locations. Two locally adapted cultivars, one resistant to H. glycines, were grown at each location. Cultivars were planted in alternating four-row strips with 76 cm between rows. For each cultivar, 20 1-m-long single-row plots were sampled every 2 weeks starting 4 weeks after planting. Infection by H. glycines reduced plant height and leaf and stem weight on the resistant cultivars in the first 12 weeks after planting, and delayed pod and seed development 12 to 14 weeks after planting. Biomass accumulation was not reduced on the susceptible cultivars until 10 weeks after planting; reduction in pod and seed development occurred throughout the reproductive stages. Susceptible cultivars produced significantly lower yields than resistant cultivars, but the yield reductions were not accompanied by visually detectable symptoms.

scholarly journals Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

2020 ◽  
Author(s):  
Aditi Bhandari ◽  
Nitika Sandhu ◽  
Jérôme Bartholome ◽  
Tuong-Vi Cao-Hamadoun ◽  
Nourollah Ahmadi ◽  
...  
Keyword(s):  
Grain Yield ◽  
Field Experiments ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Reproductive Stage ◽  
Phenotypic Variance ◽  
Rice Varieties ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

scholarly journals QTLs for resistance to soybean cyst nematode, races 3, 9, and 14 in cultivar Hartwig

2011 ◽  
Vol 46 (4) ◽  
pp. 420-428 ◽  
Author(s):  
Marcia Flores da Silva Ferreira ◽  
Gerardo Domingo Lucio Cervigni ◽  
Adésio Ferreira ◽  
Ivan Schuster ◽  
Fernanda Abreu Santana ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Cyst Nematode ◽  
Minor Effect ◽  
Phenotypic Variance ◽  
Linkage Groups ◽  
Resistance Qtls ◽  
Epistatic Interactions ◽  
Genomic Regions

The objective of this work was to identify major and minor-effect quantitative trait loci (QTL) for resistance to races 3, 9, and 14 of soybean cyst nematode (SCN) in Hartwig cultivar; to map new resistance QTLs for these races; and to check for the existence of epistatic interactions between QTLs. Cultivar Hartwig is an important resistance source to SCN. Recombinant inbred lines (RIL) obtained from a cross between 'Hartwig' (resistant) and Y23 (susceptible) were evaluated regarding resistance to the three races. New genomic regions for resistance to SCN were identified by microsatellites. Four QTLs, which explained between 12 and 34% of phenotypic variance, were detected for resistance to race 3 in linkage groups (LG) A2, G, J, and M. The QTL in LG G is also important for resistance to race 9. Epistatic interactions were detected between loci, which indicate resistance to races 9 and 14. There are high and low-effect resistance QTLs to SCN.

scholarly journals Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation

PLoS ONE ◽  
2020 ◽  
Vol 15 (7) ◽  
pp. e0235089
Author(s):  
Waltram Second Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Liana Nice ◽  
Yong Bao ◽  
...  
Keyword(s):  
Association Study ◽  
Genomic Selection ◽  
Soybean Cyst Nematode ◽  
Genome Wide Association Study ◽  
Cyst Nematode ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Selection For

Breeding a Soybean Cultivar Heinong 531 with Peking-Type Cyst Nematode Resistance, Enhanced Yield and High Seed-Oil Contents

2021 ◽  
Author(s):  
Jiajun Wang ◽  
Ling-An Kong ◽  
Liuping Zhang ◽  
Xue Shi ◽  
Baishuang Yu ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Seed Oil ◽  
Agronomic Traits ◽  
Cyst Nematode ◽  
Soybean Cultivar ◽  
High Yield ◽  
Parental Line ◽  
Average Yield ◽  
Group I ◽  
Enhanced Yield

Soybean cyst nematode (SCN) is a destructive threat to soybean production. It’s of economic importance to develop a new SCN-resistant soybean cultivar with high yield and other good agronomic traits. In this study, a yellow-seed-coated and yellow-hilum-pigmented cultivar Heinong 531 belonging to maturity group I was developed by a pedigree breeding method through a testcross between a female parental SCN-resistant soybean cultivar Pengdou 158 and a male parental line F1 (high-yield but SCN-susceptible Hefeng 55 x SCN-resistant Kangxian 12). Heinong 531 was evaluated for SCN resistance in both SCN-infested field and autoclaved soil inoculated with hatched second-stage juveniles of SCN HG Type 0. The results indicated that SCN development at all stages in Heinong 531 was suppressed and the female index was only 1.6-5.6%. Heinong 531 as well as Pengdou 158 and Kangxian 12 were identified to carry the Peking-type resistance with both rhg1-a GmSNAP18 and Rhg4 GmSHMT08 genes. In the two-year regional trials, the average yield of Heinong 531 reached 2805.0 Kg/ha and the one-year production trial demonstrated an average yield of 2751.5 Kg/ha with yield increase of over 12.0% when compared to the local cultivars. The average seed-fat (oil) contents of Heinong 531 reached up to 22.3%. The Peking-type SCN-resistant Heilong 531 cultivar with enhanced yield and high seed-oil contents was just released in China in June, 2021 with certified number of ‘Heishendou 20210004’. These good agronomic traits make Heinong 531 prospective in a wide extension to control SCN in the main soybean-producing areas of Northeast China.

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