Allelism and molecular mapping of soybean necrotic root mutants.

Mutability of the w4 flower color locus in soybean, Glycine max (L.) Merr., is conditioned by an allele designated w4-m. Germinal revertants recovered among self-pollinated progeny of mutable plants have been associated with the generation of necrotic root mutations, chlorophyll-deficiency mutations, and sterility mutations. A total of 24 necrotic root mutant lines were generated from a total of 24 independent reversion events at the w4-m locus. The initial mutable population included 4 mutable categories for w4-m, designated (1) low frequency of early excisions, (2) low frequency of late excisions, (3) high frequency of early excisions, and (4) high frequency of late excisions. These mutable categories were based upon flower phenotype, i.e., somatic tissue. A total of 22 of 24 necrotic root mutations occurred from germinal reversions classified in the high frequency of excision categories. Of these 22 mutants, 14 came from early excisions and 8 came from late excisions. These necrotic root mutants were allelic to 6 previously identified necrotic root mutants derived from the study of germinal revertants, i.e., gene tagging studies, chemical mutagenesis, and "spontaneous" occurrences from genetic crosses. Thus, all 30 necrotic root mutants in soybean are allelic. An F2 mapping population from the cross of Minsoy (Rn1 Rn1) x T328 (rn1 rn1) was used to map the Rn1 locus using simple sequence repeat (SSR) markers. The Rn1 locus was located between Satt288 and Satt612 on molecular linkage group G.     

Identification of genomic regions determining flower and pod numbers development in soybean （Glycine max L.）

Flower and pod numbers per plant are important agronomic traits underlying soybean yield.So far quantitative trait loci (QTL) detected for flower and pod-related traits have mainly focused on the final stage,and might therefore have ignored genetic effects expressed during a specific developmental stage.Here,dynamic expressions of QTL for flower and pod numbers were identified using 152 recombinant inbred lines (RILs) and a linkage map of 306 markers.Wide genetic variation was found among RILs;17 unconditional and 18 conditional QTL were detected for the two traits at different developmental stages over two years.Some QTL were detected only at one stage and others across two or more stages,indicating that soybean flower and pod numbers development may be governed by time-dependent gene expression.Three main QTL (qfn-Chr18-2,qfn-Chr20-1,and qfn-Chr19) were detected for flower number,and two main QTL (qpn-Chr11 and qpn-Chr20) were detected for pod number.The phenotypic variation explained by them ranged from 6.1% to 34.7%.The markers linked to these QTL could be used in marker-assisted selection for increasing soybean flower and pod numbers,with the ultimate aim of increasing soybean yield.Comparison of the QTL regions for flower and pod numbers traits with the related genes reported previously showed that seven and four related genes were located in the QTL regions of qfn-Chr11 and qfn-Chr19,respectively.Tbese results provide a basis for fine mapping and cloning of flower and pod development-related genes.     

QTL analysis of root traits as related to phosphorus efficiency in soybean

Background and Aims

Low phosphorus (P) availability is a major constraint to soybean growth and production, especially in tropical and subtropical areas. Root traits have been shown to play critical roles in P efficiency in crops. Identification of the quantitative trait loci (QTLs) conferring superior root systems could significantly enhance genetic improvement in soybean P efficiency.

Methods

A population of 106 F₉ recombinant inbred lines (RILs) derived from a cross between BD2 and BX10, which contrast in both P efficiency and root architecture, was used for mapping and QTL analysis. Twelve traits were examined in acid soils. A linkage map was constructed using 296 simple sequence repeat (SSR) markers with the Kosambi function, and the QTLs associated with these traits were detected by composite interval mapping and multiple-QTL mapping.

Key Results

The first soybean genetic map based on field data from parental genotypes contrasting both in P efficiency and root architecture was constructed. Thirty-one putative QTLs were detected on five linkage groups, with corresponding contribution ratios of 9·1–31·1 %. Thirteen putative QTLs were found for root traits, five for P content, five for biomass and five for yield traits. Three clusters of QTLs associated with the traits for root and P efficiency at low P were located on the B1 linkage group close to SSR markers Satt519 and Satt519-Sat_128, and on the D2 group close to Satt458; and one cluster was on the B1 linkage group close to Satt519 at high P.

Conclusions

Most root traits in soybean were conditioned by more than two minor QTLs. The region closer to Satt519 on the B1 linkage group might have great potential for future genetic improvement for soybean P efficiency through root selection.     

Duplicate chlorophyll-deficient loci in soybean.

Three lethal-yellow mutants have been identified in soybean (Glycine max (L.) Merr.), and assigned genetic type collection numbers T218H, T225H, and T362H. Previous genetic evaluation of T362H indicated allelism with T218H and T225H and duplicate-factor inheritance. Our objectives were to confirm the inheritance and allelism of T218H and T225H and to molecularly map the locus and (or) loci conditioning the lethal-yellow phenotype. The inheritance of T218H and T225H was 3 green : 1 lethal yellow in their original parental source germplasm of Glycine max 'Illini' and Glycine max 'Lincoln', respectively. In crosses to unrelated germplasm, a 15 green : 1 lethal yellow was observed. Allelism tests indicated that T218H and T225H were allelic. The molecular mapping population was Glycine max 'Minsoy' x T225H and simple sequence repeat (SSR) markers were used. The first locus, designated y18-1, was located on soybean molecular linkage group B2, between SSR markers Satt474 and Satt534, and linked to each by 4.4 and 13.4 cM, respectively. The second locus, designated y18-2, was located on soybean molecular linkage group D2, between SSR markers Satt543 and Sat-001, and linked to each by 2.2 and 4.4 cM, respectively.     

Genome mapping of white clover (<Emphasis Type="Italic">Trifolium repens</Emphasis> L.) and comparative analysis within the Trifolieae using cross-species SSR markers

Allotetraploid white clover (Trifolium repens L.), a cool-season perennial legume used extensively as forage for livestock, is an important target for marker-assisted breeding. A genetic linkage map of white clover was constructed using simple sequence repeat (SSR) markers based on sequences from several Trifolieae species, including white clover, red clover (T. pratense L.), Medicago truncatula (Gaertn.) and soybean (Glycine max L.). An F₁ population consisting of 179 individuals, from a cross between two highly heterozygous genotypes, GA43 and Southern Regional Virus Resistant, was used for genetic mapping. A total of 1,571 SSR markers were screened for amplification and polymorphism using DNA from two parents and 14 F₁s of the mapping population. The map consists of 415 loci amplified from 343 SSR primer pairs, including 83 from white clover, 181 from red clover, 77 from M. truncatula, and two from soybean. Linkage groups for all eight homoeologous chromosome pairs of allotetraploid white clover were detected. Map length was estimated at 1,877 cM with 87% genome coverage. Map density was approximately 5 cM per locus. Segregation distortion was detected in six segments of the genome (homoeologous groups A1, A2, B1, B2, C1, and D1). A comparison of map locations of markers originating from white clover, red clover, and alfalfa (M. sativa L.) revealed putative macro-colinearity between the three Trifolieae species. This map can be used to link quantitative trait loci with SSR markers, and accelerate the improvement of white clover by marker-assisted selection and breeding. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

SSR analysis of 38 genotypes of soybean (Glycine Max (L.) Merr.) genetic diversity in India

Sixteen polymorphic Simple sequence repeat (SSR) markers were used to determine the genetic diversity and varietal identification among 38 soybean (Glycine max (L.) Merr.) genotypes which are at present under seed multiplication chain in India. A total of 51 alleles with an average of 2.22 alleles per locus were detected. The polymorphic information content (PIC) among genotypes varied from 0.049 (Sat_243 and Satt337) to 0.526 (Satt431) with an average of 0.199. The pair wise genetic similarity between soybean varieties varied from 0.56 to 0.97 with an average of 0.761. These 16 SSR markers successfully distinguished 12 of the 38 soybean genotypes. These results suggest that used SSR markers are efficient for measuring genetic diversity and relatedness as well as identifying varieties of soybeans. Diverse genetic materials may be used for genetic improvements of soybean genotypes.     

Mapping genetic loci for iron deficiency chlorosis in soybean

The objective of this study was to map genes controlling iron deficiency chlorosis in two intraspecific soybean [Glycine max (L.) Merrill] populations. Chlorosis symptoms were evaluated by visual scores and spectrometric chlorophyll determinations at the V4 stage (third trifoliolate leaf fully developed) in the field in 1993, and at V2 (first trifoliolate leaf fully developed) and V4 stages in 1994. A total of 89 RFLP and 10 SSR markers in the Pride B216 x A15 population, and 82 RFLP, 14 SSR and 1 morphological I (hilum color) markers in the Anoka x A7 population were used to map quantitative trait loci (QTL) affecting iron deficiency chlorosis. QTL with minor effects were detected on six linkage groups of the Pride B216 x A15 population, suggesting a typical polygene mechanism. In contrast, in the Anoka x A7 population, one QTL contributed an average of 72.7% of the visual score variation and 68.8% of the chlorophyll concentration variation and was mapped on linkage group N. Another QTL for visual score variation, and one for chlorophyll concentration variation were detected on linkage groups A1 and I, respectively. Due to the large LOD score and major genetic effect of the QTL on linkage group N, the quantitative data was reclassified into qualitative data fitting a one major gene model according to the means of the QTL genotypic classes. The major gene was mapped in the same interval of linkage group N using both visual scores and chlorophyll concentrations, thus verifying that one major gene is involved in segregation for iron chlorosis deficiency in the Anoka x A7 population. This study supported a previous hypothesis that two separate genetic mechanisms control iron deficiency in soybean.     

Genetic linkage mapping of the soybean aphid resistance gene in PI 243540

The soybean aphid (Aphis glycines Matsumura) is a pest of soybean [Glycine max (L.) Merr.] in many soybean growing countries of the world, mainly in Asia and North America. A single dominant gene in PI 243540 confers resistance to the soybean aphid. The objectives of this study were to identify simple sequence repeat (SSR) markers closely linked to the gene in PI 243540 and to position the gene on the consensus soybean genetic map. One hundred eighty-four F(2) plants and their F(2:3) families from a cross between the susceptible cultivar Wyandot and PI 243540, and the two parental lines were screened with the Ohio biotype of soybean aphid using greenhouse choice tests. A SSR marker from each 10-cM section of the consensus soybean map was selected for bulked segregant analysis (BSA) to identify the tentative genomic location of the gene. The BSA technique was useful to localize the gene to a genomic region in soybean linkage group (LG) F. The entire F(2) population was then screened with polymorphic SSR markers from this genomic region and a linkage map with nine SSR markers flanking the gene was constructed. The aphid resistance gene was positioned in the interval between SSR markers Satt334 and Sct_033 on LG F. These SSR markers will be useful for marker assisted selection of this gene. The aphid resistance gene from PI 243540 mapped to a different linkage group than the only named soybean aphid resistance gene, Rag1, from 'Dowling'. Also, the responses of the two known biotypes of the soybean aphid to the gene from PI 243540 and Rag1 were different. Thus, the aphid resistance gene from PI 243540 was determined to be a new and independent gene that has been named Rag2.     

Inheritance of growth habit detected by genetic linkage analysis using microsatellites in the common bean (Phaseolus vulgaris L.)

The genetic linkage map for the common bean (Phaseolus vulgaris L.) is a valuable tool for breeding programs. Breeders provide new cultivars that meet the requirements of farmers and consumers, such as seed color, seed size, maturity, and growth habit. A genetic study was conducted to examine the genetics behind certain qualitative traits. Growth habit is usually described as a recessive trait inherited by a single gene, and there is no consensus about the position of the locus. The aim of this study was to develop a new genetic linkage map using genic and genomic microsatellite markers and three morphological traits: growth habit, flower color, and pod tip shape. A mapping population consisting of 380 recombinant F10 lines was generated from IAC-UNA × CAL143. A total of 871 microsatellites were screened for polymorphisms among the parents, and a linkage map was obtained with 198 mapped microsatellites. The total map length was 1865.9 cM, and the average distance between markers was 9.4 cM. Flower color and pod tip shape were mapped and segregated at Mendelian ratios, as expected. The segregation ratio and linkage data analyses indicated that the determinacy growth habit was inherited as two independent and dominant genes, and a genetic model is proposed for this trait.     

QTL mapping of domestication-related traits in soybean (Glycine max)

BACKGROUND AND AIMS: Understanding the genetic basis underlying domestication-related traits (DRTs) is important in order to use wild germplasm efficiently for improving yield, stress tolerance and quality of crops. This study was conducted to characterize the genetic basis of DRTs in soybean (Glycine max) using quantitative trait locus (QTL) mapping. METHODS: A population of 96 recombinant inbred lines derived from a cultivated (ssp. max) x wild (ssp. soja) cross was used for mapping and QTL analysis. Nine DRTs were examined in 2004 and 2005. A linkage map was constructed with 282 markers by the Kosambi function, and the QTL was detected by composite interval mapping. KEY RESULTS: The early flowering and determinate habit derived from the max parent were each controlled by one major QTL, corresponding to the major genes for maturity (e1) and determinate habit (dt1), respectively. There were only one or two significant QTLs for twinning habit, pod dehiscence, seed weight and hard seededness, which each accounted for approx. 20-50 % of the total variance. A comparison with the QTLs detected previously indicated that in pod dehiscence and hard seededness, at least one major QTL was common across different crosses, whereas no such consistent QTL existed for seed weight. CONCLUSIONS: Most of the DRTs in soybeans were conditioned by one or two major QTLs and a number of genotype-dependent minor QTLs. The common major QTLs identified in pod dehiscence and hard seededness may have been key loci in the domestication of soybean. The evolutionary changes toward larger seed may have occurred through the accumulation of minor changes at many QTLs. Since the major QTLs for DRTs were scattered across only six of the 20 linkage groups, and since the QTLs were not clustered, introgression of useful genes from wild to cultivated soybeans can be carried out without large obstacles.     

Genetic and linkage analysis of purple-blue flower in soybean

Flower color of soybean is primarily controlled by genes W1, W3, W4, Wm, and Wp. In addition, the soybean gene symbol W2, w2 produces purple-blue flower in combination with W1. This study was conducted to determine the genetic control of purple-blue flower of cultivar (cv). Nezumisaya. F(1) plants derived from a cross between Nezumisaya and purple flower cv. Harosoy had purple flowers. Segregation of the F(2) plants fitted a ratio of 3 purple:1 purple-blue. F(3) lines derived from F(2) plants with purple-blue flowers were fixed for purple-blue flowers, whereas those from F(2) plants with purple flowers fitted a ratio of 1 fixed for purple flower:2 segregating for flower color. These results indicated that the flower color of Nezumisaya is controlled by a single gene whose recessive allele is responsible for purple-blue flower. Complementation analysis revealed that flower color of Nezumisaya is controlled by W2. Linkage mapping revealed that W2 is located in molecular linkage group B2. Sap obtained from banner petals of cvs. with purple flower had a pH value of 5.73-5.77, whereas that of cvs. with purple-blue flower had a value of 6.07-6.10. Our results suggested that W2 is responsible for vacuolar acidification of flower petals.     

Identification of QTLs for seed and pod traits in soybean and analysis for additive effects and epistatic effects of QTLs among multiple environments

Soybean seed and pod traits are important yield components. Selection for high yield style in seed and pod along with agronomic traits is a goal of many soybean breeders. The intention of this study was to identify quantitative trait loci (QTL) underlying seed and pod traits in soybean among eleven environments in China. 147 recombinant inbred lines were advanced through single-seed-descent method. The population was derived from a cross between Charleston (an American high yield soybean cultivar) and DongNong594 (a Chinese high yield soybean cultivar). A total of 157 polymorphic simple sequence repeat markers were used to construct a genetic linkage map. The phenotypic data of seed and pod traits [number of one-seed pod, number of two-seed pod, number of three-seed pod, number of four-seed pod, number of (two plus three)-seed pod, number of (three plus four)-seed pod, seed weight per plant, number of pod per plant] were recorded in eleven environments. In the analysis of single environment, fourteen main effect QTLs were identified. In the conjoint analysis of multiple environments, twenty-four additive QTLs were identified, and additive QTLs by environments interactions (AE) were evaluated and analyzed at the same time among eleven environments; twenty-three pairs of epistatic QTLs were identified, and epistasis (additive by additive) by environments interactions (AAE) were also analyzed and evaluated among eleven environments. Comparing the results of identification between single environment mapping and multiple environments conjoint mapping, three main effect QTLs with positive additive values and another three main effect QTLs with negative additive values, had no interactions with all environments, supported that these QTLs could be used in molecular assistant breeding in the future. These different effect QTLs could supply a good foundation to the gene clone and molecular asisstant breeding of soybean seed and pod traits.     

Genomic selection in soybean: accuracy and time gain in relation to phenotypic selection

Genomic selection (GS) can potentially accelerate genetic improvement of soybean [Glycine max L. (Merrill)] by reducing the time to complete breeding cycles. The objectives of this study were to (1) explore the accuracy of GS in soybean, (2) evaluate the contribution of intrapopulational structure to the accuracy of GS, and (3) compare the efficiencies of phenotypic selection and GS in soybean. For this, phenotypic and genotypic data were collected from 324 soybean genotypes (243 recombinant inbred lines and 81 cultivars) and GS was performed for five yield related traits. BayesB methodology with a 10-fold cross-validation was used to compute accuracies. The GS accuracies were evaluated for grain yield, plant height, insertion of first pod, days to maturity, and 1000-grain weight at eight locations. We found that GS can reduce the time required to complete a selection cycle in soybean, which can lead to increased production of this commercially important crop. Furthermore, genotypic accuracy was similar regardless of population structure correction.     

Soybean molecular linkage group B1 corresponds to classical linkage group 16 based on map location of the <Emphasis Type="Italic">lf</Emphasis><Subscript>2</Subscript> gene

The seven-leaflet character of soybean [Glycine max L. (Merr.)] is a single recessive trait conditioned by the lf ( 2 ) gene. The lf ( 2 ) gene is located on linkage group (LG) 16 of the classical soybean genetic map, but it has not been placed on the molecular map. The objective of this research was to identify the location of the lf ( 2 ) gene on the soybean molecular map using simple sequence repeat (SSR) markers. A backcross breeding method was used to create three- and seven-leaflet near-isogenic lines in genetic backgrounds of 'Traill', 'MN1401', and 'MN1801'. Eight mapping populations were derived from eight single heterozygous Lf ( 2 ) lf ( 2 ) plants. A total of 482 SSR markers that covered approximately every 10-20 cM of all soybean molecular LG were used to screen the mapping populations for polymorphisms. For the 115 SSRs that were identified as polymorphic, possible linkage between the lf ( 2 ) gene and the polymorphic SSR markers was determined. One SSR marker from the LG B1, Sat_272, was linked (LOD > 4.0) to the lf ( 2 ) gene in the Traill and MN1401 derived populations, with map distances ranging from 2.8 to 11.2 cM. Two additional markers (a SSR, Sat_270 and a SNP, A588c) located on LG B1 were also polymorphic and were identified as linked to the lf ( 2 ) gene in one of the populations. This research was successful in mapping the lf ( 2 ) gene to LG B1 of the soybean molecular map and therefore, provides evidence that molecular LG B1 corresponds to classical LG 16.     

Mapping of the genomic regions controlling seed storability in soybean (Glycine max L.)

Seed storability is especially important in the tropics due to high temperature and relative humidity of storage environment that cause rapid deterioration of seeds in storage. The objective of this study was to use SSR markers to identify genomic regions associated with quantitative trait loci (QTLs) controlling seed storability based on relative germination rate in the F_2:3 population derived from a cross between vegetable soybean line (MJ0004-6) with poor longevity and landrace cultivar from Myanmar (R18500) with good longevity. The F_2:4 seeds harvested in 2011 and 2012 were used to investigate seed storability. The F₂ population was genotyped with 148 markers and the genetic map consisted of 128 SSR loci which converged into 38 linkage groups covering 1664.3 cM of soybean genome. Single marker analysis revealed that 13 markers from six linkage groups (C1, D2, E, F, J and L) were associated with seed storability. Composite interval mapping identified a total of three QTLs on linkage groups C1, F and L with phenotypic variance explained ranging from 8.79 to 13.43%. The R18500 alleles increased seed storability at all of the detected QTLs. No common QTLs were found for storability of seeds harvested in 2011 and 2012. This study agreed with previous reports in other crops that genotype by environment interaction plays an important role in expression of seed storability.     

Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation

Microsatellite or single sequence repeat (SSR) markers have been commonly used in genetic research in many crop species, including common bean (Phaseolus vulgaris L.). A limited number of existing SSR markers have been designed from high-throughput sequencing of the genome, warranting the exploitation of new SSR markers from genomic regions. In this paper, we sequenced total DNA from the genotype Hong Yundou with a 454-FLX pyrosequencer and found numerous SSR loci. Based on these, a large number of SSR markers were developed and 90 genomic-SSR markers with clear bands were tested for mapping and diversity detection. The new SSR markers proved to be highly polymorphic for molecular polymorphism, with an average polymorphism information content value of 0.44 in 131 Chinese genotypes and breeding lines, effective for distinguishing Andean and Mesoamerican genotypes. In addition, we integrated 85 primers of the 90 polymorphism markers into the bean map using an F2 segregating population derived from Hong Yundou crossed with Jingdou. The distribution of SSR markers among 11 chromosomes was not random and tended to cluster on the linkage map, with 14 new markers mapped on chromosome Pv01, whereas only four loci were located on chromosome Pv04. Overall, these new markers have potential for genetic mapping, genetic diversity studies and map-based cloning in common bean.     

Identification of simple sequence repeat markers linked to lipoxygenase-1 gene in soybean

Off-flavour generated in soy products is ascribed to soybean seed lipoxygenase-1, lipoxygenase-2 and lipoxygenase-3, controlled by single dominant genes Lox1, Lox2 and Lox3, respectively. Lox2 locus has already been mapped and reported to be tightly linked with Lox1 locus. The objective of the present study was to map Lox1 locus by investigating the SSR markers reported to be linked with Lox2 locus and the neighbouring SSR markers in two mapping populations of 116 and 91 plants developed from LSb1 × PI408251 and JS335 × PI408251, respectively. Parental polymorphism was surveyed using SSR markers Sat_074, Satt522 reported to be linked with Lox2 locus and the SSR markers in its proximity. F_2:3 seeds were used for assaying lipoxygenase-1 to identify the genotype of the F₂ individuals. SSR marker Satt656 was found to be tightly linked with Lox1 locus at distance of 3.6 and 4.8 cM in the mapping population of LSb1 × PI408251 and JS335 × PI408251, respectively. SSR marker Satt656 can be useful for marker assisted selection for transferring recessive allele of lipoxygenase-1 in the background of high yielding soybean genotypes.     

Mapping genes conferring resistance to Phytophthora root rot of soybean, Rps1a and Rps7.

A linkage map was constructed for two Phytophthora sojae Kauf. +Gerd. root rot resistance genes, Rps1a and Rps7, in soybean (Glycine max (L.) Merr.) using microsatellite or simple sequence repeat (SSR) markers. An F2 population consisting of 81 individuals derived from a cross between OX281, which carries Rps7, and Mukden, which carries Rps1a, was used as the mapping population. A linkage map consisting of 10 SSR markers was first constructed using the computer software MapMaker/EXP 3.0. Rps1a and Rps7 were then placed at two different loci in the same linkage group with LOD scores of 2.88 and 9.16, respectively. Rps1a and Rps7 were linked at a distance of 13.8 cM. Rps1a was flanked by Satt159 (0.7 cM) and Satt009 (3.2 cM). Rps7 was flanked by Satt009 (10.6 cM) and Satt125 (29.1 cM).