ABSTRACT
Nitrogen (N) fixation in soybean Glycine max (L.) Merr. is more sensitive to drought than photosynthesis, and high concentrations of shoot ureide and N are associated with sensitivity of N2 ...fixation to drought. Genotypic differences in ureide and N concentration were evaluated using a mapping population of 97 recombinant inbred lines derived from a cross between ‘KS4895’ and ‘Jackson’. For three irrigated environments, broad‐sense heritability for ureide and N concentration was 0.73 and 0.59, respectively. Under irrigated conditions, five quantitative trait loci (QTLs) for ureide concentration were identified using composite interval mapping (CIM). Multiple interval mapping (MIM) identified two QTLs with locations similar to those identified with CIM. Four QTLs for N concentration were detected using CIM, and one QTL was identified with MIM with a similar position as that identified with CIM. A QTL on Gm13 for shoot ureide and N appeared to be pleiotropic. In the drought environment, two QTLs were identified using CIM for both shoot ureide and N; a QTL for ureide concentration on Gm19 mapped to the same position as a ureide QTL under irrigated conditions, but the additive effect was opposite in sign. A search for metabolic genes in QTL regions predicted for the pleiotropic effect of N and ureide (Gm13, carbonic anhydrase) and for ureide (Gm19, inosine–uridine nucleoside hydrolase). These QTLs may be useful in selecting lines drought tolerant for N2 fixation.
We have estimated the average genetic diversity of two
annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for ...departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11
accessions. Among the perennials,
showed the highest nucleotide diversity. The other perennials, except for
, had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the
showed a similar genome grouping with the previous report except for
and
which formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships that
was the most divergent from
, followed by
,
,
D3,
and
Most genic sequences were homogeneous in the levels of polymorphism and divergence between
and other
species based on the HKA test, thus,
perennials may have experienced a very similar evolution as inferred by
-specific mutation analysis. The greater genetic diversity of most perennial
species and their origins from the warmer and drier climates of Australia suggests the perennials maybe a potential source of heat and drought resistance that will be of value in the face of climate change.
Soybean
Glycine max
(L.) Merr. is an important crop which contributes approximately 58% of the world’s oilseed production. Palmitic and stearic acids are the two main saturated fatty acids in ...soybean oil. Different levels of saturated fatty acids are desired depending on the uses of the soybean oil. Vegetable oil low in saturated fatty acids is preferred for human consumption, while for industrial applications, soybean oil with higher levels of saturated fatty acids is more suitable. The objectives of this study were to identify quantitative trait loci (QTL) for saturated fatty acids, analyze the genetic effects of single QTL and QTL combinations, and discuss the potential of marker-assisted selection in soybean breeding for modified saturated fatty acid profiles. A population of recombinant inbred lines derived from the cross of SD02-4-59 × A02-381100 was grown in five environments and the seed samples from each environment were evaluated for fatty acid content. Genotyping of the population was performed with 516 polymorphic single nucleotide polymorphism markers and 298 polymorphic simple sequence repeat markers. Eight QTL for palmitic acid, five QTL for stearic acid and nine QTL for total saturated fatty acids were detected by composite interval mapping and/or interval mapping, with a high level of consistency or repeatability in multiple environments. Most of these QTL have not been reported previously, with the exception of
qPAL
-
A1
which confirmed the result of a previous study. Significant QTL × QTL interactions were not detected. However, significant QTL × environment interactions were detected in most cases. Comparisons of two-locus and three-locus combinations indicated that cumulative effects of QTL were significant for both palmitic and stearic acids. QTL pyramiding by molecular marker-assisted selection would be an appropriate strategy for improvement of saturated fatty acids in soybean.
Soybean (Glycine max (L.) Merr.) is a major source of plant protein for humans and livestock. Deficiency of sulfur-containing amino acids (cysteine and methionine) in soybean protein is a main ...limitation of soybean meal as an animal feed ingredient. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with cysteine and methionine contents in two recombinant inbred line (RIL) populations, and to analyze the genetic effects of individual QTLs and QTL combinations in soybean. Both the mapping population of SD02-4-59 × A02-381100 and validation population of SD02-911 × SD00-1501 were evaluated for cysteine and methionine contents in multiple environments. Correlation analysis indicated that there was a highly positive correlation between cysteine and methionine contents. Significant positive correlations were also observed between the sulfur-containing amino acid contents and protein content. In the mapping population, eight QTLs for both cysteine and methionine contents were consistently detected in any individual environment and the average data over all three environments. Three of these QTLs were confirmed in the validation population. A comparison with the previous studies indicated that most of the genomic regions linked to the QTLs for the sulfur-containing amino acids were also associated with protein content. Cumulative effects of multiple QTLs for the traits were significant in both populations. This information should be useful for the improvement of the levels of protein and amino acids in soybean seeds.
ABSTRACT
Empoasca species leafhoppers are a major insect pest of common bean (Phaseolus vulgaris L.), that cause significant economic losses in both tropical (E. kraemeri) and temperate (E. fabae) ...regions of the Americas. The objective of this study was to use Insertion–Deletion (InDel) and single‐nucleotide polymorphism (SNP) markers from the BARCBean6K_3 Beadchip to identify quantitative trait loci (QTL) associated with traits related to leafhopper resistance in common bean. Traits for leaf curl and leaf burn damage, as well as Empoasca spp. nymph counts, were evaluated in an inbred backcross line population (Matterhorn*/EMP507) of beans in temperate (Michigan) and tropical (Puerto Rico) climates. Fourteen QTL associated with resistance to E. fabae and E. kraemeri were identified on five chromosomes explaining up to 66.0% of the phenotypic variation for single resistance traits. A major QTL cluster associated with multiple resistance traits and closely linked to the P color gene was detected for both leafhopper species in multiple seasons under both choice and no‐choice treatments on Pv07 (LH7.1, LH7.2, LH7.3), thus validating a similar QTL identified in previous studies. A novel QTL (LH2.2) for E. fabae nymph counts, identified on Pv02 in three seasons, may be associated with antibiosis resistance. Resistance to each leafhopper species appears to be controlled by separate genetic mechanisms in common bean as there was little overlap of QTL regions between species. These QTL could be used to develop beans with leafhopper resistance as an alternative to costly chemical controls while reducing risks to the environment and human health.
Soybean aphid (
Aphis glycines
Matsumura) has become one of the major pests of soybean
Glycine max
(L.) Merr. in North America since 2000. At least four biotypes of soybean aphid have been confirmed ...in the United States. Genetic characterization of new sources of soybean aphid resistance will facilitate the expansion of soybean gene pool for soybean aphid resistance and thus will help to develop soybean aphid resistant cultivars. To characterize the genetic basis of soybean aphid resistance in PI 603712, a newly identified resistant germplasm line, 142 F
2
plants derived from the cross ‘Roberts’ × PI 603712 and their parents were evaluated for soybean aphid resistance in the greenhouse, and were genotyped with BARCSoySNP6K Illumina Infinium II BeadChip. A genome-wide molecular linkage map was constructed with 1495 polymorphic SNP markers. QTL analysis revealed that PI 603712 possessed two major loci associated with soybean aphid resistance, located on chromosome 7 and 16, respectively. The locus on chromosome 7 was dominantly expressed and positioned about one Mega-base-pair distant from the previously identified resistance locus
Rag1
. The locus on chromosome 16 was positioned near the previously identified resistance locus
Rag3
and expressed partially dominance or additive effect. Interestingly, two minor loci were also detected on chromosomes 13 and 17 but the alleles from PI 603712 decreased the resistance. In developing soybean aphid resistant cultivars through marker-assisted selection, an appropriate combination of resistance loci should be selected when PI 603712 is used as a donor parent of resistance.
Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) ...accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.
ABSTRACT
Common bacterial blight (CBB) is a severe disease in common bean (Phaseolus vulgaris L.). New resistance quantitative trait loci (QTL) should facilitate development of cultivars with high ...levels of resistance. Our objectives were to (i) identify new resistance QTL in VAX 1 and verify its presence in VAX 3, (ii) determine the interaction between QTL with existing SAP6 and SU91 QTL, and (iii) examine the interaction between QTL with less aggressive ARX8AC and aggressive Xcp25 bacterial strains. Sixty‐one F6:7 recombinant inbred lines (RIL) from ‘Othello’/VAX 1 and 100 RIL from Othello/VAX 3 were screened in the greenhouse. Disease severity of inoculated primary leaves, first and second trifoliolate leaves, and pods, was scored from 1 = no symptoms to 9 = completely diseased. Genotyping was performed using 5398 single nucleotide polymorphism (SNP) BeadChip and CBB resistance QTL‐linked sequence characterized amplified region (SCAR) markers, SAP6 and SU91. A novel resistance QTL with major effect was detected on Pv11 linkage group in Othello/VAX 1 and verified in Othello/VAX 3. This Pv11 QTL, defined by the closest marker SNP47467 (45,059,806 bp), explained 23% of the phenotypic variance for resistance in primary and 18% in trifoliolate leaves in Othello/VAX 1, and 13% and 22%, respectively, in Othello/VAX 3 to ARX8AC. The Pv11 QTL, named Xa11.4OV1,OV3, had greater influence against Xcp25, with respective values for variance for resistance explained in primary and trifoliolate leaves of 45% and 51% in Othello/VAX 1 and 26% and 37% in Othello/VAX 3. Conversely, SAP6 was only effective against ARX8AC in both populations, and surprisingly, SU91 was only effective against Xcp25 in Othello/VAX 3. SAP6 was the only QTL to condition resistance in pods. QTL interactions and differential reactions to strains indicate that the new Xa11.4OV1,OV3 QTL is critical in breeding for stable and higher levels of foliage resistance to CBB in common bean.
KEY MESSAGE : The Rag2 region was frequently identified among 21 F ₂ populations evaluated for soybean aphid resistance, and dominant gene action and single-gene resistance were also commonly ...identified. The soybean aphid Aphis glycines Matsumura (Hemiptera: Aphididae) is one of the most important insect pests of soybean Glycine max (L.) Merr in the northern USA and southern Canada, and four resistance loci (Rag1–rag4) have been discovered since the pest was identified in the USA in 2000. The objective of this research was to determine whether resistance expression in recently identified soybean aphid-resistant plant introductions (PIs) was associated with the four Rag loci using a collection of 21 F₂ populations. The F₂ populations were phenotyped with soybean aphid biotype 1, which is avirulent on plants having any of the currently identified Rag genes, using choice tests in the greenhouse and were tested with genetic markers linked to the four Rag loci. The phenotyping results indicate that soybean aphid resistance is controlled by a single dominant gene in 14 PIs, by two genes in three PIs, and four PIs had no clear Mendelian inheritance patterns. Genetic markers flanking Rag2 were significantly associated with aphid resistance in 20 PIs, the Rag1 region was significantly identified in five PIs, and the Rag3 region was identified in one PI. These results show that single dominant gene action at the Rag2 region may be a major source for aphid resistance in the USDA soybean germplasm collection.
Phytophthora root rot (PRR) has long been a serious disease impacting soybean production in the U.S.A. The use of PRR resistant soybean varieties has and continues to be the best approach to combat ...this disease. The use of genetic markers to identify breeding lines that carry resistance to PRR avoids the need to conduct laborious greenhouse screening tests to identify lines that are resistant to PRR. Thus, the objective of this research was to determine the genetic control of resistance to PRR in the highly resistant soybean line E00003 and then to find genetic markers that can be used to identify breeding lines that carry the resistance gene(s) in E00003. A total of 240 breeding lines derived from a cross of E00003 with a PRR susceptible soybean were analyzed for resistance to PRR using three different races of PRR. The breeding lines were also analyzed with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) DNA markers in order to find DNA markers associated with the gene(s) controlling resistance to PRR. PRR resistance was determined to be controlled by one major gene and two SSR and three SNP DNA markers were found to be closely associated with the gene. The resistance gene was determined to be the Rps1k gene. The SSR and SNP markers in close proximity to the gene can be used by soybean breeders to identify soybean breeding lines that carry the Rps1k resistance gene.
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