Multigeneic QTL: The Laccase Encoded within the Soybean Rfs2/rhg1 Locus Inferred to Underlie Part of the Dual Resistance to Cyst Nematode and Sudden Death Syndrome

Multigeneic QTL present significant problems to analysis. Resistance to soybean (Glycine max (L) Merr.) sudden death syndrome (SDS) caused by Fusarium virguliforme was partly underlain by QRfs2 that was clustered with, or pleiotropic to, the multigeneic rhg1 locus providing resistance to soybean cyst nematode (SCN; Heterodera glycines ). A group of five genes were found between the two markers that delimited the Rfs2/rhg1 locus. One of the five genes was predicted to encode an unusual diphenol oxidase (laccase; EC 1.10.3.2). The aim of this study was to characterize this member of the soybean laccase gene-family and explore its involvement in SDS resistance. A genomic clone and a full length cDNA was isolated from resistant cultivar \u27Forrest\u27 that were different among susceptible cultivars \u27Asgrow 3244\u27 and \u27Williams 82\u27 at four residues R/H168, I/M271, R/H330, E/K470. Additional differences were found in six of the seven introns and the promoter region. Transcript abundance (TA) among genotypes that varied for resistance to SDS or SCN did not differ significantly. Therefore the protein activity was inferred to underlie resistance. Protein expressed in yeast pYES2/NTB had weak enzyme activity with common substrates but good activity with root phenolics. The Forrest isoform may underlie both QRfs 2 and rhg

Genetic Analysis of Relative Water Content (RWC) in Two Recombinant Inbred Line Populations of Soybean [Glycine max (L.) Merr.]

Drought affects soybean [Glycine max (L.) Merr.] and other crops productivity in the US and other parts of the world. Relative water content (RWC) is an important indicator for plant water deficit tolerance (WDT). The objective of this study is to map quantitative trait loci (QTL) for RWC and several other leaf traits such as leaf dry weight (LDW), leaf fresh weight (LFW), and leaf turgid weight (LTW) in two soybean recombinant inbred line (RIL) populations, one derived from a cross of ‘Essex’ and ‘Forrest’ (ExF, n=94) and the other is derived from a cross of ‘PI 438489B’ and ‘Hamilton’ (PIxH, n=50). In the PIxH RIL population, eight QTL were identified and mapped on 6 different linkage groups (LGs) of the soybean genome. No QTL for LFW were identified in this population. In the ExF RIL population, 10 QTL were identified and mapped on 5 different LGs of soybean. Chromosome 18 (LG G) contains clusters of QTL for LFW, LTW, and RWC in the ExF RIL population. This same chromosome contains a QTL for RWC in the PIxH RIL population. The QTL found here are important to be included in breeding programs for soybean water deficit tolerance (WDT)

Quantitative Trait Loci Underlying Seed Sugars Content in “MD96-5722” by “Spencer” Recombinant Inbred Line Population of Soybean

Sucrose, raffinose, and stachyose are important soluble sugars in soybean [Glycine max (L.) Merr.] seeds. Seed sucrose is a desirable trait for taste and flavor. Raffinose and stachyose are undesirable in diets of monogastric animals, acting as anti-nutritional factors that cause flatulence and abdominal discomfort. Therefore, reducing raffinose and stachyose biosynthesis is considered as a key quality trait goal in soy food and feed industries. The objective of this study was to identify genomic regions containing quantitative trait loci (QTL) controlling sucrose, raffinose, and stachyose in a set of 92 F5:7 recombinant inbred lines (RILs) derived from a cross between the lines “MD96- 5722” and “Spencer” by using 5376 Single Nucleotide Polymorphism (SNP) markers from the Illumina Infinium SoySNP6K BeadChip array. Fourteen significant QTL were identified and mapped on eight different linkage groups (LGs) and chromosomes (Chr). Three QTL for seed sucrose content were identified on LGs N (Chr3), K (Chr9), and E (Chr15). Seven QTL were identified for raffinose content on LGs D1a (Chr1), N (Chr3), C2 (Chr6), K (Chr9), B2 (Chr14), and J (Chr16). Four QTL for stachyose content were identified on LG D1a (Chr1), C2 (Chr6), H (Chr12), and B2 (Chr14). Selection for beneficial alleles of these QTLs could facilitate breeding strategies to develop soybean lines with higher concentrations of sucrose and lower levels of raffinose and stachyose

Identification of Quantitative Trait Loci (QTL) Underlying Protein, Oil, and Five Major Fatty Acids’ Contents in Soybean

Improved seed composition in soybean [Glycine max (L.) Merr.] for protein and oil quality is one of the major goals of soybean breeders. A group of genes that act as quantitative traits with their effects can alter protein, oil, palmitic, stearic, oleic, linoleic, and linolenic acids percentage in soybean seeds. The objective of this study was to identify Quantitative Trait Loci (QTL) controlling protein, oil, and fatty acids content in a set of F5:8 RILs de-rived from a cross between lines, ‘MD 96-5722’ and ‘Spencer’ using 5376 Single Nucleotide Polymorphism (SNP) markers from the Illumina Infinium SoySNP6K BeadChip array. QTL analysis used WinQTL Cart 2.5 software for composite interval mapping (CIM). Identified, were; one protein content QTL on linkage group (LG-) B2 or chromosome (Chr_) 14; 11 QTL associated with oil content on six linkage groups LG-N (Chr_3), LG-A1 (Chr_5), LG-K (Chr_9), LG-F (Chr_13), LG-B2 (Chr_14), and LG-J (Chr_16); and sixteen QTL for five major fatty acids (palmitic, stearic, oleic, linoleic, and linolenic acids) on LG-N (Chr_3), LG-F (Chr_13), LG-B2 (Chr_14), LG-E (Chr_15), LG-J (Chr_16), and LG-G (Chr_18). The SNP markers closely linked to the QTL reported here will be useful for development of cultivars with altered oil and fatty acid compositions in soybean breeding programs

Genetic Analysis of Root and Shoot Traits in the ‘Essex’ By ‘Forrest’ Recombinant Inbred Line (RIL) Population of Soybean [Glycine max (L.) Merr.]

Crop productivity is severely reduced by water deficit and drought in many plant species including soybean. Improved root and shoot traits can contribute to drought tolerance ability of the plant. This research was conducted to identify QTL that underlie several root and shoot traits in the ‘Essex’ by ‘Forrest’ (ExF RILs, n=94) recombinant inbred line (RIL) soybean population. Field collected samples were used for gathering phenotypic data of basal root thickness (BRT), lateral root number (LRN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW), and calculating RFW/SFW, and RDW/SDW ratios. All traits and ratios were compared against DNA markers using the composite interval mapping (CIM). A total of 12 QTL: 3 for MRL, 1 QTL for LRN, 1 QTL for BRT, 2 QTL for RFW, 2 QTL for RDW, 4 QTL for SFW, 3 QTL for SDW, and 3 QTL for SFW/SDW were identified and mapped on different linkage groups (LGs) A2, B2, C2, D1a, F, G, and N. The LOD scores of these QTL ranged from 2.5 to 6.0. No QTL were associated with RFW/RDW. The root and shoot trait QTL of this study may benefit breeding programs for producing cultivars tolerant to water deficit and high yield. Preliminary analyses of genes the QTL regions using GO annotation gave insight into genes that may underlie some of these QTLs

Definition of Soybean Genomic Regions That Control Seed Phytoestrogen Amounts

Soybean seeds contain large amounts of isoflavones or phytoestrogens such as genistein, daidzein, and glycitein that display biological effects when ingested by humans and animals. In seeds, the total amount, and amount of each type, of isoflavone varies by 5 fold between cultivars and locations. Isoflavone content and quality are one key to the biological effects of soy foods, dietary supplements, and nutraceuticals. Previously we had identified 6 loci (QTL) controlling isoflavone content using 150 DNA markers. This study aimed to identify and delimit loci underlying heritable variation in isoflavone content with additional DNA markers. We used a recombinant inbred line (RIL) population ([Formula: see text]) derived from the cross of “Essex” by “Forrest,” two cultivars that contrast for isoflavone content. Seed isoflavone content of each RIL was determined by HPLC and compared against 240 polymorphic microsatellite markers by one-way analysis of variance. Two QTL that underlie seed isoflavone content were newly discovered. The additional markers confirmed and refined the positions of the six QTL already reported. The first new region anchored by the marker BARC_Satt063 was significantly associated with genistein ([Formula: see text] , [Formula: see text]) and daidzein ([Formula: see text] , [Formula: see text]). The region is located on linkage group B2 and derived the beneficial allele from Essex. The second new region defined by the marker BARC_Satt129 was significantly associated with total glycitein ([Formula: see text] , [Formula: see text]). The region is located on linkage group D1a+Q and also derived the beneficial allele from Essex. Jointly the eight loci can explain the heritable variation in isoflavone content. The loci may be used to stabilize seed isoflavone content by selection and to isolate the underlying genes

SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array

This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean

Genomic regions that underlie soybean seed isoflavone content

Soy products contain isoflavones (genistein, daidzein, and glycitein)that display biological effects when ingested by humans and animals, these effects are species, dose and age dependent. Therefore, the content and quality of isoflavones in soybeans is a key to their biological effect. Our objective was to identify loci that underlie isoflavone content in soybean seeds. The study involved 100 recombinant inbred lines (RIL)fr om the cross of ‘Essex’ by ‘Forrest,’ two cultivars that contrast for isoflavone content. Isoflavone content of seeds fromeach RIL was determined by high performance liquid chromatography (HPLC). The distribution of isoflavone content was continuous and unimodal. The heritability estimates on a line mean basis were 79% for daidzein, 22% for genistein, and 88% for glycitein. Isoflavone content of soybean seeds was compared against 150 polymorphic DNA markers in a one-way analysis of variance. Four genomic regions were found to be significantly associated with the isoflavone content of soybean seeds across both locations and years. Molecular linkage group B1 contained a major QTL underlying glycitein content (P = 0.0001,R2 = 50.2%), linkage group N contained a QTL for glycitein (P = 0.0033,R2 = 11.1%)and a QTL for daidzein (P = 0.0023,R2 = 10.3%) and linkage group A1 contained a QTL for daidzein (P = 0.0081,R2 = 9.6%). Selection for these chromosomal regions in a marker assisted selection program will allow for the manipulation of amounts and profiles of isoflavones (genistein, daidzein, and glycitein)c ontent of soybean seeds. In addition, tightly linked markers can be used in map based cloning of genes associated with isoflavone content

Additional Quantitative Trait Loci and Candidate Genes for Seed Isoflavone Content in Soybean

Seed isoflavone content of soybean (Glycine max L. Merr.) is a trait of moderate heritablity and an ideal target for marker selection. To date over 20 QTL have been identified underlying this trait among seven populations. The objectives of this study were to identify additional QTL and candidate genes controlling isoflavone content in a set of recombinant inbred line (RIL) populations of soybean grown in two different seasons. Variations of isoflavones namely daidzein, glycitein and genistein contents over two growing seasons and locations suggests that isoflavones are influenced by both genes and environments. Six QTL were identified on five different chromosomes (Chr) or linkage groups (LG) that controlled daidzein (Chr_2/LG-M; Chr_17a/LG-D2), glycitein (Chr_2/LG-D1b; Chr_8/LG-A2) and genistein (Chr_8/LG-A2; Chr_12/LG-H) respectively in the seeds grown in season 2010. Two QTL were identified for daidzein (Chr_6/LG-C2; Chr_13b/LG-F), two QTLs for glycitein (Chr_1/LG-D1a; Chr_17c/LG-D2) and five QTLs for genistein (Chr_3/ LG-N; Chr_8/LG-A2; Chr_9/LG-K; Chr_18/LG-G) in the seeds of the 2011 growing season. Genes located within QTL confidence intervals were retrieved and gene ontology (GO) terms were used to identify those related to the flavonoid biosynthesis process. Twenty six candidate genes were identified that may be involved in isoflavones accumulation in soybean seeds

The soybean GmSNAP18 gene underlies two types of resistance to soybean cyst nematode

Two types of resistant soybean (Glycine max (L.) Merr.) sources are widely used against soybean cyst nematode (SCN, Heterodera glycines Ichinohe). These include Peking-type soybean, whose resistance requires both the rhg1-a and Rhg4 alleles, and PI 88788-type soybean, whose resistance requires only the rhg1-b allele. Multiple copy number of PI 88788-type GmSNAP18, GmAAT, and GmWI12 in one genomic segment simultaneously contribute to rhg1-b resistance. Using an integrated set of genetic and genomic approaches, we demonstrate that the rhg1-a Peking-type GmSNAP18 is sufficient for resistance to SCN in combination with Rhg4. The two SNAPs (soluble NSF attachment proteins) differ by only five amino acids. Our findings suggest that Peking-type GmSNAP18 is performing a different role in SCN resistance than PI 88788-type GmSNAP18. As such, this is an example of a pathogen resistance gene that has evolved to underlie two types of resistance, yet ensure the same function within a single plant species