HG Type Research Articles

RNA-seq-based identification of potential resistance genes against the soybean cyst nematode (Heterodera glycines) HG Type 1.2.3.5.7 in ‘Dongnong L-10’

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a parasitic plant pathogenic nematode that severely affects the growth and development of soybean. Breeding SCN-resistant varieties is one of the safest and most effective ways to manage SCN. ‘Dongnong L-10’ is a well-known SCN-resistant variety in Northeast China, but the molecular mechanisms governing this resistance have not been determined. Hence, in this study, we transcriptome sequenced the roots of ‘Dongnong L-10’ (Resistant varieties of SCN race 4) and ‘Heinong 37’ (Susceptible varieties of SCN race 4) under the stress of HG Type 1.2.3.5.7 (SCN race 4). We obtained a total of 76.75 GB of the raw reads. A total of 4400 and 5724 differentially expressed genes (DEGs) were related to the SCN resistance of ‘Dongnong L-10’ and ‘Heinong 37’. The analysis of DEGs showed that transcription factors (AP2/EREBP, WRKY, MYB, NAC, bHLH and C2H2) and plant hormone signal transduction pathways (the jasmonic acid and salicylic acid pathways) may be involved in the response of soybean to HG Type 1.2.3.5.7. RT-qPCR analysis showed that the relative expression levels of PR protein family gene GmRSCN4-1 (Glyma.05G204800) and cytochrome P450 family gene GmRSCN4-2 (Glyma.16G195600) in ‘Dongnong L-10’ were significantly higher than those in ‘Heinong 37’. Overexpression of GmRSCN4-1 and GmRSCN4-2 in soybean hairy roots resulted in increased HG Type 1.2.3.5.7 resistance in soybean hairy roots. Our results not only provide a theoretical basis for analyzing the resistance mechanism of ‘Dongnong L-10’ to HG Type 1.2.3.5.7, but also provide some genes resources for soybean molecular breeding for resistance to cyst nematode.

Genetic characterization of qSCN10 from an exotic soybean accession PI 567516C reveals a novel source conferring broad-spectrum resistance to soybean cyst nematode.

The qSCN10 locus with broad-spectrum SCN resistance was fine-mapped to a 379-kb region on chromosome 10 in soybean accession PI 567516C. Candidate genes and potential application benefits of this locus were discussed. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pests of soybean, causing significant yield losses worldwide every year. Genetic resistance has been the major strategy to control this pest. However, the overuse of the same genetic resistance derived primarily from PI 88788 has led to the genetic shifts in nematode populations and resulted in the reduced effectiveness in soybean resistance to SCN. Therefore, novel genetic resistance resources, especially those with broad-spectrum resistance, are needed to develop new resistant cultivars to cope with the genetic shifts in nematode populations. In this study, a quantitative trait locus (QTL) qSCN10 previously identified from a soybean landrace PI 567516C was confirmed to confer resistance to multiple SCN HG Types. This QTL was further fine-mapped to a 379-kb region. There are 51 genes in this region. Four of them are defense-related and were regulated by SCN infection, suggesting their potential role in mediating resistance to SCN. The phylogenetic and haplotype analyses of qSCN10 as well as other information indicate that this locus is different from other reported resistance QTL or genes. There was no yield drag or other unfavorable traits associated with this QTL when near-isogenic lines with and without qSCN10 were tested in a SCN-free field. Therefore, our study not only provides further insight into the genetic basis of soybean resistance to SCN, but also identifies a novel genetic resistance resource for breeding soybean for durable, broad-spectrum resistance to this pest.

RNA-Seq analysis of resistant and susceptible soybean genotypes in response to stress from soybean cyst nematode (

The soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is a major disease affecting soybean (Glycine max (L.) Merr.) production and yield. Breeding of new SCN-resistant cultivars and understanding their resistance mechanisms are valuable for improving SCN resistance of soybean. However, we still know little about resistance mechanisms to SCN. The purpose of our analysis was to understand the different resistance mechanisms of resistant and susceptible lines to SCN by dissecting their transcriptional changes during infection by SCN HG type 1.2.3.5.7. In this study, 119 recombinant inbred lines derived from a cross of cv. Dongnong L-204 (SCN resistant) and cv. Heinong 37 (SCN susceptible) were identified for resistance status to SCN HG type 1.2.3.5.7. Roots of the lines identified as extremely resistant or susceptible (L5, L89) were sequenced by transcriptome, and we obtained 66.61 Gb of data. Compared with the untreated control, there were 8394 and 6899 differentially expressed genes in SCN-infected roots of L5 and L89, respectively. Genes of metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction, and plant–pathogen interaction pathway were significantly expressed in both resistant and susceptible genotypes. The expression of genes of phenylpropanoid biosynthesis, flavonoid biosynthesis, thiamine metabolism, cutin, suberin and wax biosynthesis, and endocytosis pathway was significantly higher in the resistant line than the susceptible line. Transcription factor analysis showed that 88 transcription factors from 18 transcription factor families responded to SCN stress. Nine genes were identified by reverse transcriptase qPCR to be associated with SCN resistance. This study helps us to understand better the mechanism of soybean resistance to SCN.

머신비전 기법을 이용한 발광박테리아(Vibrio fischeri) 생태독성 분석법 개발

In this study, we propose a methodd to determine ecotoxicity more conveniently than conventional testing methods using luminometer for vibrio fischeri bioassay introduced in 2017. The device to be developed is to detect the luminous intensity of the luminescence bacteria in a dark room of 15oC for 30 minutes, and store them as data, and use machine vision, one of the artificial intelligence techniques, to determine and predict toxicity. For this purpose, three types of heavy metals, Cu, Pb and Hg, and perfluorinated compounds PFOS (Heptadecafluorooctaneulphonic acid solution, ~40% in (T)) were used. The results of ecological toxicity assessment through digital image processing were measured very similarly to those using conventional Luminometer. Although it is somewhat insufficient to generalize as an experiment on four toxic substances, it has been proposed that practical devices that can measure ecological toxicity using luminous bacteria can be developed relatively simply through experiments on various substances in the future.

A new black bean with resistance to bean rust: Registration of ‘ND Twilight’

Abstract‘ND Twilight’ (Reg. no. CV‐332, PI 693268; PVP‐202000258) is a new black bean (Phaseolus vulgaris L.) cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. ND Twilight was developed using a modified pedigree method (F1–F5), followed by pure line selection based on agronomic, disease, and quality traits, along with specific DNA markers. With ∼24% of the total dry bean production in the United States, black bean is the second most important market class after pinto. Accounting for ∼35% of the total production, North Dakota is the largest producer of dry bean in the United States. However, both biotic and abiotic stresses are the main factors responsible for seed yield reductions. Between 2014 and 2019, ND Twilight was tested across more than 21 environments in North Dakota, where seed yield was significantly different from ‘Zorro’ and similar to ‘Eclipse’ and ‘Loreto’. ND Twilight is resistant to the most common race (20‐3) of the bean rust pathogen and Bean common mosaic virus. It also has intermediate resistance to common bacterial blight and to soybean cyst nematode (HG Type 0). ND Twilight has desirable upright architecture (Type IIa). Under North Dakota conditions, ND Twilight shows an average plant height of 49 cm, has a 100‐seed weight of 19.7 g, and matures in ∼99 d. Canning quality was rated as acceptable. Other traits of agronomic and economic importance are within acceptable commercial ranges.

Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C.

The qSCN18 QTL from PI 56756C was confirmed and fine-mapped to improve soybean resistance to the SCN population HG Type 2.5.7 using near-isogenic lines carrying recombination crossovers within the QTL region. The QTL underlying resistance was fine-mapped to a 166-Kbp region on chromosome 18, and the candidate genes were selected based on genomic analyses. Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) is the most devastating pathogen of soybean. Understanding the genetic basis of SCN resistance is crucial for managing this parasite in the field. Two major loci, rhg1 and Rhg4, were previously characterized as valuable resources for SCN resistance. However, their continuous use has caused shifts in the virulence of SCN populations, which can overcome the resistance conferred by these two major loci. Reduced effectiveness became a major concern in the soybean industry due to continuous use of rhg1 for decades. Thus, it is imperative to identify sources of SCN resistance for durable SCN management. A novel QTL qSCN18 was identified in PI567516C. To fine-map qSCN18 and identify resistance genes, a large backcross population was developed. Nineteen near-isogenic lines (NILs) carrying recombination crossovers within the QTL region were identified. The first phase of fine-mapping narrowed the QTL region to 549-Kbp, whereas the second phase confined the region to 166-Kbp containing 23 genes. Two flanking markers, MK-1 and MK-6, were developed and validated to detect the presence of the qSCN18 resistance allele. Haplotype analysis clustered the fine-mapped qSCN18 region from PI 567516C with the cqSCN-007 locus previously mapped in the wild soybean accession PI 468916. The NILs were developed to further characterize the causal gene(s) harbored in this QTL. This study also confirmed the previously identified qSCN18. The results will facilitate marker-assisted selection (MAS) introducing the qSCN18 locus from PI 567516C into high-yielding soybean cultivars with durable resistance to SCN.

Registration of ‘S14‐15138GT’ soybean as a high‐yielding RR1/STS cultivar with broad disease resistance and adaptation

Abstract‘S14‐15138GT’ (Reg. no. CV‐537, PI 693754) is a late maturity group IV (relative maturity 4.8) indeterminate high‐yielding soybean [Glycine max (L) Merr.] cultivar with glyphosate and sulfonylurea tolerance developed and released in 2017 by the University of Missouri–Fisher Delta Research Center soybean breeding program. S14‐15138GT is an F4 plant selection from the cross ‘S09‐10871’ × ‘S08‐9727RR1’. S14‐15138GT was tested in 83 environments across 11 states and showed high yield potential and wide adaptation in Missouri and other southern states. In the University of Missouri yield trials, S14‐15138GT yielded, on average, 110% of the tests mean across 19 locations in 4 yr (2015–2018). Plants of S14‐15138GT are 84 cm tall and have white flower color, tawny pubescence, and tan pod walls. On average, S14‐15138GT seed contains 406 g kg−1 protein and 221 g kg−1 oil on a dry seed weight basis. S14‐15138GT has a broad disease resistance package including resistance to soybean cyst nematode races 3 and 14 (HG Type 5.7 and Type 1.3.6.7), stem canker, frogeye leaf spot, sudden death syndrome, and phomopsis seed decay. In addition to its high yield potential, strong disease resistance package, and broad adaptation, S14‐15138GT is a suitable alternative for farmers who want to grow and save seed of glyphosate‐tolerant soybean cultivars.

A Process Mineralogical Evaluation of Chromite at the Nkomati Nickel Mine, Uitkomst Complex, South Africa

A process mineralogical study based on three texturally and mineralogically different chromite-bearing ore types at the Nkomati nickel mine was undertaken, with focus on chromite. Chromite is a by-product of the Ni-Cu-Co-PGE ore at Nkomati Nickel mine. These being the PCMZ_MG (medium-grade Ni-Cu sulphide silicate ore with disseminated chromite), PCMZ_HG (high-grade Ni-Cu sulphide silicate ore containing disseminated chromite) and MCHR (massive chromite unit) ore types. These were processed using benchtop flotation followed by gravity concentration using a shaking table at different grind sizes. Quantitative mineralogical data was obtained using a 600F Mineral Liberation Analyser for the unprocessed and processed ores at three selected target grinds. The Mineral Liberation Analyser data indicated that increased milling does not relate to increased chromite grades and recoveries, particularly for the disseminated PCMZ type ores based on laboratory-scale gravity concentration. The recovery is controlled largely by the chromite chemistry. The results also showed that the MCHR samples that underwent a pre-flotation stage before gravity separation had better Cr2O3 grades (45% to 47%) and recoveries (52% to 61%) than MCHR ore that did not undergo a pre-flotation stage, which recorded grades ranging from 44% to 46% and recoveries ranging from 43% to 60%. This holds promise for the blending of MCHR ores with the PCMZ ores. The PCMZ ores also displayed better Cr2O3 grades and recoveries at coarser grinds. The optimal target grind to process all three ore types is a P80 of 75 μm, which is the current grind size employed at Nkomati Nickel mine. Due to the low nickel price and grade the Nkomati Nickel mine is currently under care and maintenance.

Structural analyses of the HG-type pectin from notopterygium incisum and its effects on galectins

In the manuscript, water-soluble polysaccharides WPNI was extracted from notopterygium incisum roots and separated into two homogeneous fractions WPNI-A-a and WPNI-A-b. WPNI-A-a was an arabinogalactan (AG). WPNI-A-b belonged to HG type pectin. The structure of WPNI-A-b was analyzed by FT-IR, NMR, enzymatic hydrolysis (Endo-PG) and UPLC-FLD-MSn. WPNI-A-b was dominated by HG domain, covalently linked with AG and RG-II domains. Oligogalacturonides produced by Endo-PG from HG domain were non-, mono-, di- or tri-methyl esterified with degree of polymerization (DP) from 1 to 6. The distribution of methyl-ester groups was in a block-wise manner. The interaction of WPNI-A-b and its enzymatic hydrolysis products with galectin-1, galectin-3, galectin-7 and galectin-8 showed that AG domain exhibited stronger binding avidity to galectins than RG-II and HG domain, while oligogalacturonides showed no binding activities to galectins. The results would be useful for the application of the pectin from notopterygium incisum.

Characterizing resistance to soybean cyst nematode in PI 494182, an early maturing soybean accession

AbstractThe soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) generates more damage to soybean [Glycine max (L.) Merr.] than any other parasite in most soybean‐producing countries. The use of SCN‐resistant cultivars remains the most effective method to limit losses caused by SCN. The SCN‐resistant accession PI 88788 has been used almost exclusively to control SCN over the past decades, inducing a shift in nematode virulence to overcome the resistance. Furthermore, PI 88788 and other sources of resistance characterized to date belong to maturity groups (MGs) III and higher, making them less attractive to develop early maturing soybean varieties (MGs 0‐000). In this work, we performed a quantitative trait loci (QTL) analysis of the SCN‐resistant soybean accession PI 494182 (MG 0). A recombinant inbred lines (RILs) population (‘Costaud’ × PI 494182) segregating for SCN resistance was challenged with SCN (H. glycines [HG] type 0) and genotyped via genotyping‐by‐sequencing (GBS) to produce a genetic map. Six resistance QTL were identified, including a potentially new resistance locus on chromosome 07. A subset of the RIL population was confronted to a HG type 2.5.7 SCN population and some of these exhibited resistance toward this type. Whole‐genome sequencing of PI 494182 and Costaud allowed us to determine the alleles and their copy number for three candidate genes: GmSNAP11, GmSNAP18 (Rhg1), and GmSHMT08 (Rhg4). Finally, we determined that selecting for PI 494182 alleles at some SCN‐resistance QTL could entail linkage drag (decrease in protein concentration and 100‐seed weight, increase in oil concentration). This work provides useful markers for introgressing SCN resistance in early maturing soybean varieties.

Evaluation of diverse cover crops as hosts of two populations of soybean cyst nematode, Heterodera glycines

Soybean cyst nematode (SCN; Heterodera glycines) reproduces on a wide range of plants, including some cover crops. However, reproduction of SCN populations on a number of cover crops has not been investigated in the northern Great Plains. Thirty-five cover crop species/cultivars from four plant families were evaluated as hosts for SCN. Greenhouse evaluations were done with two common SCN populations, SCN103 (HG type 0) and SCN2W (HG type 7) under controlled conditions. The sources of two SCN populations were two soybean fields of North Dakota. After 35 days of growth, white SCN females were extracted from individual plants and counted to determine a female index (FI = average number of females on a tested crop/average number of females in a susceptible check x 100) for each crop. Out of the 35 cover crop species/cultivars tested, at least one of the SCN populations reproduced on seven crops/cultivars but did not reproduce on the other 28 crops/cultivars. Out of these seven crops, only white lupine (Lupinus albus L.) was a suitable host (FI ≥ 10) for both SCN populations in all the experiments, while others showed varied responses from poor host to suitable host for the SCN populations. The host crops were from the family Brassicaceae or Fabaceae, while all the crops in the Linaceae or Poaceae family tested were non-hosts. The non-host crops can be planted in SCN-infested fields without the concern of increasing SCN populations, while poor hosts with low female index should be evaluated for effects on reduction of SCN numbers in the fields before they are used as cover crops in a soybean cropping system.

‘ND Falcon’, a new pinto bean with combined resistance to rust and soybean cyst nematode

Abstract‘ND Falcon’ pinto bean (PVP‐201900174, Reg. no. CV‐326, PI 690446) is a new cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. Pinto bean is the most important dry bean market class in the United States. North Dakota is the largest producer of dry bean in the country, where ∼50% of production is pinto bean. Both biotic and abiotic stresses are the main factors responsible for seed yield reductions. Between 2013 and 2018, ND Falcon was tested across more than 22 environments in North Dakota. Averaged across environments, seed yield of ND Falcon was not significantly different from commonly grown pinto bean cultivars in the region. Nonetheless, ND Falcon is resistant to the most common race (20‐3) of the bean rust pathogen and to soybean cyst nematode (HG Type 0). Therefore, a seed yield advantage under disease pressure would be expected for ND Falcon compared with other pinto bean cultivars while eliminating or reducing the need for fungicide and/or nematicide applications. ND Falcon has desirable upright architecture (type IIa) with short vines. Under North Dakota conditions, ND Falcon shows an average plant height of 53 cm, has a 100‐seed weight of 37.0 g, and matures in approximately 103 d. Other traits of agronomic or economic importance are within acceptable commercial ranges for pinto bean.

Screening and characterization of high-quality and high-yield <italic>japonica</italic> rice varieties in Yanhuai region of Anhui province

<p indent="0mm">A field experiment was conducted with 74 conventional <italic>japonica</italic> rice varieties (lines), which were divided into four types according to the yield and taste value, i.e. high yield with good quality (HG), high yield with bad quality (HB), medium yield with good quality (MG), and medium yield with bad quality (MB). Among them, HG, HB, MG were weed to analyze their yield, quality differences and characteristics in HG formation, providing a scientific basis and theoretical support for screening, planting and extending the suitable varieties in Yanhuai area of Anhui province. The yield of MG was 16.95%, 16.76%, and 16.52%, 16.33% lower than that of HG type and HB type, respectively in 2017 and 2018. In 2017, compared with HB type, HG and MG types decreased by 39.31% and 42.63% in amylose content, increased by 22.06% and 19.12% in length of gel consistency, and decreased by 11.60% and 17.78% in protein content. The characteristics of these HG<italic> japonica</italic> rice varieties were mainly as follows: the yield was <sc>8.35–9.16 t</sc> hm^–2, the number of panicles per unit area was 310×10⁴–320×10⁴ hm^–2, the grain number per panicle was around 140, the 1000-grain weight was over <sc>25 g;</sc> the taste value was 60–74, the length of gel consistency was <sc>80–90 mm,</sc> and the protein content was between 6% and 8%.

RNA-Seq-based identification of potential resistance mechanism against the soybean cyst nematode (Heterodera glycines) HG Type 0 in soybean (Glycine max) cv. Dongnong L-204

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most important disease affecting yield of soybean (Glycine max (L.) Merr.). In China, among the main physiological races of SCN causing serious economic loss of soybean, HG Type 0 is the most widely distributed. Breeding SCN-resistant varieties is one of the safest and most effective ways to manage SCN. Soybean cv. Dongnong L-204 has a green seed coat and is a resource for resistance to SCN; however, the transcriptional variation and main molecular mechanism of resistance of Dongnong L-204 are not clear. We obtained 66.42 Gb of raw reads by using Illumina HiSeq high-throughput sequencing of Dongnong L-204. Transcriptional changes at Days 3, 7 and 10 after HG Type 0 stress are described. In total, 11279 differentially expressed genes were responsive to HG Type 0 stress, including 6407 SCN-induced and 4872 SCN-suppressed genes. Gene Ontology analysis emphasised the important roles of the terms metabolic process, single-organism process, catalytic activity and binding under HG Type 0 stress. Among them, the terms related to extracellular matrix, extracellular region part, membrane-enclosed lumen, protein-binding transcription factor activity, and symplast and cell junction existed only in pairwise comparisons Day 7 vs Day 0 and Day 10 vs Day 0. KEGG enrichment analysis showed that metabolic pathway played an important role in the stress response to HG Type 0. Cellular processes, metabolism and organismal systems and other pathway-related genes increased significantly after 7 days. Transcription factor analysis showed that transcription factors such as MYB, AP2-EREBP, bHLH, WRKY and NAC may be involved in the anti-HG Type 0 response of Dongnong L-204. At the same time, few transient inducible transcription factors were found and more transient inhibited transcription factors in Dongnong L-204 in the early stage of HG Type 0 syncytial establishment. RT-qPCR was used to analyse expression of 10 genes closely related to the HG Type 0 stress response. The expression of GmWRKYX1 was &amp;gt;60 times higher at Day 10 after HG Type 0 stress than at Day 0. The WRKY transcription-factor family may play an important role in the resistance of Dongnong L-204 to HG Type 0 stress.

Registration of TN15‐4009 soybean germplasm with resistance to soybean cyst nematode, southern root knot nematode, and peanut root knot nematode

AbstractThe conventional (non‐genetically modified) soybean [Glycine max (L.) Merrill] line TN15‐4009 (Reg. no. GP‐437, PI 691608) was released by University of Tennessee Agricultural Research in 2019 as a germplasm line on the basis of its high seed yield potential in the southern region of the United States and resistance to soybean cyst nematode (SCN), southern root knot nematode, and peanut root knot nematode. The objective of its development was to create a high‐yielding SCN‐resistant soybean line. Progeny rows were selected based on adapted maturity, lodging resistance, disease resistance, and pod density and were entered in yield tests from 2015 through 2018. TN15‐4009 has white flowers and tawny pubescence. The pods have a tan pod wall, and the seed is yellow with a smooth seed coat. The seed size is approximately 13.6 g 100 seed−1, which was significantly greater than that of ‘Ellis’ in the 2018 USDA Uniform Test. In that test, TN15‐4009 matured 1 d earlier than Ellis and the same as ‘AG 4835’, indicating that the relative maturity of TN15‐4009 is approximately 4.8. Soybean line TN15‐4009 is resistant to SCN HG type 5.7 (score = 1) and HG type 2.5.7 (score = 1), resistant to southern root knot nematode (score = 1), and resistant to peanut root knot nematode (score = 1.3). TN15‐4009 is susceptible to stem canker.

The effects of Meloidogyne incognita and Heterodera glycines on the yield and quality of edamame (Glycine max l.) in Arkansas.

In 2012, the first domestic commercial edamame processing plant was established in Arkansas and edamame production was contracted out to local growers. Although the state is a major soybean producer, studies of nematode effects on edamame are limited. A survey of nematode genera and density in 64 contracted edamame production fields was conducted in 2013 and 2014. In both years, Meloidogyne and Heterodera were present in less than half of the surveyed fields while Pratylenchus was the most prevalent in 2013 and Helicotylenchus in 2014. A microplot study was conducted in 2014 in two locations to evaluate the effects of root-knot nematode (Meloidogyne incognita, race 3) and soybean cyst nematode (Heterodera glycines, HG type 2.5.7) on plant growth, yield and food quality components of edamame. Yield was the most consistent factor influenced by nematode pressure with increasing nematode population densities resulting in suppressed pod and seed weight. Additionally, seed protein content was reduced in the highest tested population density of H. glycines. In greenhouse studies, 22 advanced edamame breeding lines from the University of Arkansas soybean breeding program were compared with two susceptible commercial cultivars for suitability as hosts for both M. incognita and H. glycines independently. Four lines showed consistent reductions in M. incognita reproduction relative to the commercial cultivars and could represent sources of moderate resistance for development of future root-knot nematode resistant edamame cultivars.

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

BackgroundDomestication 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.ResultsThis 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.ConclusionsAlthough 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.

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

BackgroundSoybean 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.ResultsA 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.ConclusionsIn 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.

Early transcriptional responses to soybean cyst nematode HG Type 0 show genetic differences among resistant and susceptible soybeans.

Root transcriptome profiling of three soybean cultivars and a wild relative infected with soybean cyst nematode at migratory phase revealed differential resistance pathway responses between resistant and susceptible genotypes. The soybean cyst nematode (SCN), Heterodera glycines, is the most serious pathogen of soybean production throughout the world. Using resistant cultivars is the primary management strategy against SCN infestation. To gain insight into the still obscure mechanisms of genetic resistance to nematodes in different soybean genotypes, RNA-Seq profiling of the roots of Glycine max cv. Peking, Fayette, Williams 82, and a wild relative (Glycine soja PI 468916) was performed during SCN infection at the migratory phase. The analysis showed statistically significant changes of expression beginning at eight hours after inoculation in genes associated with defense mechanisms and pathways, such as the phenylpropanoid biosynthesis pathway, plant innate immunity and hormone signaling. Our results indicate the importance of the early plant response to migratory phase nematodes in pathogenicity determination. The transcriptome changes occurring during early SCN infection included a number of genes and pathways specific to the different resistant genotypes. We observed the most extensive resistant transcriptome reaction in PI 468916, where the resistant response was qualitatively different from that of commonly used G. max varieties.

Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean

Soybean aphid (Aphis glycines; SBA) and soybean cyst nematode (Heterodera glycines; SCN) are two major pests of soybean (Glycine max) in the United States of America. This study aims to characterize three-way interactions among soybean, SBA, and SCN using both demographic and genetic datasets. SCN-resistant and SCN-susceptible soybean cultivars with a combination of soybean aphids (biotype 1) and SCN (HG type 0) in a randomized complete block design (RCBD) with six blocks were used to evaluate the three-way interactions in a greenhouse setup. Treatments receiving SCN were infested at planting with 2000 nematode eggs, and the treatments with soybean aphids were infested at second trifoliate growth stage (V2) with 15 soybean aphids. The whole roots were sampled from plants at 5 and 30 days post SBA infestation for RNA sequencing using Illumina Hiseq. 3000. The data comprises of 47 libraries that are useful for further analyses of important genes, which are involved in interaction effects of SBA and SCN on soybean.