SSR mapping and confirmation of the QTL from PI96354 conditioning soybean resistance to southern root-knot nematode

Root-knot nematodes (Meloidogyne spp.) can cause severe yield loss of soybean [Glycine max (L.) Merr.] in the southern production region of the USA. Planting root-knot nematode-resistant cultivars is the most effective method of preventing yield loss. DNA marker-assisted breeding may accelerate the development of root-knot nematode-resistant cultivars. RFLP markers have previously been used to identify quantitative trait loci (QTLs) conferring resistance to southern root-knot nematode [Meloidogyne incognita (Kofoid and White) Chitwood] (Mi) in a F_2:3 soybean population created by crossing the resistant PI96354 and the susceptible ’Bossier.’ A major QTL on linkage group (LG) O conditioning 31% of the variation in Mi gall number and a minor QTL on LG-G conditioning 14% of the gall variation were reported. With the development of SSR markers for soybean improvement, a higher level of mapping resolution and semi-automated detection has become possible. The objectives of this research were: (1) to increase the marker density in the genomic regions of the QTLs for Mi resistance on LG-O and LG-G with SSR markers; and (2) to confirm the effect of the QTLs in a second population and a different genetic background. With SSR markers, the QTL on LG-O was flanked by Satt492 and Satt358, and on LG-G by Satt012 and Satt505. Utilizing SSR markers flanking the two QTLs, marker-assisted selection was performed in a second F_2:3 population of PI96354× Bossier. Results confirmed the effectiveness of marker-assisted selection to predict the Mi phenotypes. By screening the BC₂F₂ population of Prichard (3)×G93–9009 we confirmed that selection for the minor QTL on LG-G with flanking SSR markers would enhance the resistance of lines containing the major QTL (which is most-likely Rmi1). Received: 29 September 2000 / Accepted: 17 April 2001     

Pyramiding multiple genes for resistance to soybean mosaic virus in soybean using molecular markers

Seven strains of Soybean mosaic virus (SMV) and three independent resistance loci (Rsv1, Rsv3, and Rsv4) have been identified in soybean. The objective of this research was to pyramid Rsv1, Rsv3, and Rsv4 for SMV resistance using molecular markers. J05 carrying Rsv1 and Rsv3 and V94-5152 carrying Rsv4 were used as the donor parents for gene pyramiding. A series of F_2:3, F_3:4, and F_4:5 lines derived from J05 × V94-5152 were developed for selecting individuals carrying all three genes. Eight PCR-based markers linked to the three SMV resistance genes were used for marker-assisted selection. Two SSR markers (Sat_154 and Satt510) and one gene-specific marker (Rsv1-f/r) were used for selecting plants containing Rsv1; Satt560 and Satt063 for Rsv3; and Satt266, AI856415, and AI856415-g for Rsv4. Five F_4:5 lines were homozygous for all eight marker alleles and presumably carry all three SMV resistance genes that would potentially provide multiple and durable resistance to SMV.     

Soybean aphid resistance genes in the soybean cultivars Dowling and Jackson map to linkage group M

The soybean aphid [Aphis glycines Matsumura] is an important pest of soybean [Glycine max (L.) Merr.] in North America. Single dominant genes in the cultivars ‘Dowling’ and ‘Jackson’ control resistance to the soybean aphid. The gene in Dowling was named Rag1, and the genetic relationship between Rag1 and the gene in Jackson is not known. The objectives of this study were to map the locations of Rag1 and the Jackson gene onto the soybean genetic map. Segregation of aphid resistance and simple sequence repeat (SSR) markers in F _2:3 populations developed from crosses between Dowling and the two susceptible soybean cultivars ‘Loda’ and ‘Williams 82’, and between Jackson and Loda, were analyzed. Both Rag1 and the Jackson gene segregated 1:2:1 in the F _2:3 populations and mapped to soybean linkage group M between the markers Satt435 and Satt463. Rag1 mapped 4.2 cM from Satt435 and 7.9 cM from Satt463. The Jackson gene mapped 2.1 cM from Satt435 and 8.2 cM from Satt463. Further tests to determine genetic allelism between Rag1 and the Jackson gene are in progress. The SSR markers flanking these resistance genes are being used in marker-assisted selection for aphid resistance in soybean breeding programs. Trade and manufacturers’ names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.     

Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds

Soybean [Glycine max (L.) Merr.] is the single largest source of protein in animal feed. However, a major limitation of soy proteins is their deficiency in sulfur-containing amino acids, methionine (Met) and cysteine (Cys). The objective of this study was to identify quantitative trait loci (QTL) associated with Met and Cys concentration in soybean seed. To achieve this objective, 101 F₆-derived recombinant inbred lines (RIL) from a population developed from a cross of N87-984-16 × TN93-99 were used. Ground soybean seed samples were analyzed for Met and Cys concentration using a near infrared spectroscopy instrument. Data were analyzed using SAS software and QTL Cartographer. RIL differed (P<0.01) in Met and Cys concentrations, with a range of 5.1–7.3 (g kg⁻¹ seed dry weight) for Cys and 4.4–8.8 (g kg⁻¹ seed dry weight) for Met. Heritability estimates on an entry mean basis were 0.14 and 0.57 for Cys and Met, respectively. A total of 94 polymorphic simple sequence repeat molecular genetic markers were screened in the RIL. Single factor ANOVA was used to identify candidate QTL, which were confirmed by composite interval mapping using QTL Cartographer. Four QTL linked to molecular markers Satt235, Satt252, Satt427 and Satt436 distributed on three molecular linkage groups (MLG) D1a, F and G were associated with Cys and three QTL linked to molecular markers Satt252, Satt564 and Satt590 distributed on MLG F, G and M were associated with Met concentration in soybean seed. QTL associated with Met and Cys in soybean seed will provide important information to breeders targeting improvements in the nutritional quality of soybean.     

Validation of SSR markers linked to null kunitz tryspin inhibitor allele in Indian soybean [Glycine max (L.) Merr.] population

Kunitz trypsin inhibitor, a proteinaceous antinutritional factor present in soybean seeds, is responsible for inferior nutritional quality of raw soybean and incompletely processed soy products. The objective of the present investigation was to validate the SSR markers (Satt228 and Satt409) reported to be linked to Ti locus in an Indian soybean population generated from the cross between soybean cultivar LSb1 (TiTi) and PI542044 (titi). Parental polymorphism was surveyed using Satt409, Satt228 and 5 SSR markers in the neighbouring genomic region of Ti locus. A portion of the cotyledon of F₂ seeds was used for analyzing the presence or absence of kunitz trypsin inhibitor polypeptide electrophoretically while the remaining portion containing the embryo was used for raising the F₂ plants (104) for the development of mapping population. The SSR marker Satt228 reported to be tightly linked with Ti locus was not found to be polymorphic for the parents used in our study. Satt409 was found to be linked with Ti locus at 4.7 cM. Besides, a new marker Satt538 was found to be linked with Ti locus at a distance of 17.8 cM. Thus, the SSR marker Satt409 can be useful for Marker Assisted Selection for transferring titi allele in the background of Indian soybean genotypes.     

Mapping Isoflavone QTL with Main,Epistatic and QTL × Environment Effects in Recombinant Inbred Lines of Soybean

Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F_5:6, F_5:7 and F_5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar ‘Zhong Dou 27′ (high isoflavone) and ‘Jiu Nong 20′ (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM with mean distance of about 12 cM between markers was constructed. Thirty four QTL for both individual and total seed isoflavone contents of soybean were identified. Six, seven, ten and eleven QTL were associated with daidzein (DZ), glycitein (GC), genistein (GT) and total isoflavone (TI), respectively. Of them 23 QTL were newly identified. The qTIF_1 between Satt423 and Satt569 shared the same marker Satt569 with qDZF_2, qGTF_1 and qTIF_2. The qGTD2_1 between Satt186 and Satt226 was detected in four environments and explained 3.41%-10.98% of the phenotypic variation. The qGTA2_1, overlapped with qGCA2_1 and detected in four environments, was close to the previously identified major QTL for GT, which were responsible for large a effects. QTL (qDZF_2, qGTF_1 and qTIF_2) between Satt144-Satt569 were either clustered or pleiotropic. The qGCM_1, qGTM_1 and qTIM_1 between Satt540-Sat_244 explained 2.02%–9.12% of the phenotypic variation over six environments. Moreover, the qGCE_1 overlapped with qGTE_1 and qTIE_1, the qTIH_2 overlapped with qGTH_1, qGCI_1 overlapped with qDZI_1, qTIL_1 overlapped with qGTL_1, and qTIO_1 overlapped with qGTO_1. In this study, some of unstable QTL were detected in different environments, which were due to weak expression of QTL, QTL by environment interaction in the opposite direction to a effects, and/or epistasis. The markers identified in multi-environments in this study could be applied in the selection of soybean cultivars for higher isoflavone content and in the map-based gene cloning.     

Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (<Emphasis Type="Italic">Cajanus</Emphasis> spp.)

Single feature polymorphisms (SFPs) are microarray-based molecular markers that are detected by hybridization of DNA or cRNA to oligonucleotide probes. With an objective to identify the potential polymorphic markers for drought tolerance in pigeonpea [Cajanus cajan (L.) Millspaugh], an important legume crop for the semi-arid tropics but deficient in genomic resources, Affymetrix Genome Arrays of soybean (Glycine max), a closely related species of pigeonpea were used on cRNA of six parental genotypes of three mapping populations of pigeonpea segregating for agronomic traits like drought tolerance and pod borer (Helicoverpa armigiera) resistance. By using robustified projection pursuit method on 15 pair-wise comparisons for the six parental genotypes, 5,692 SFPs were identified. Number of SFPs varied from 780 (ICPL 8755 × ICPL 227) to 854 (ICPL 151 × ICPL 87) per parental combination of the mapping populations. Randomly selected 179 SFPs were used for validation by Sanger sequencing and good quality sequence data were obtained for 99 genes of which 75 genes showed sequence polymorphisms. While associating the sequence polymorphisms with SFPs detected, true positives were observed for 52.6% SFPs detected. In terms of parental combinations of the mapping populations, occurrence of true positives was 34.48% for ICPL 151 × ICPL 87, 41.86% for ICPL 8755 × ICPL 227, and 81.58% for ICP 28 × ICPW 94. In addition, a set of 139 candidate genes that may be associated with drought tolerance has been identified based on gene ontology analysis of the homologous pigeonpea genes to the soybean genes that detected SFPs between the parents of the mapping populations segregating for drought tolerance.     

Identification of QTL for increased fibrous roots in soybean

Drought stress adversely affects soybean at various developmental stages, which collectively results in yield reduction. Unpredictable rainfall has been reported to contribute about 36% to variation of yield difference between the rain-fed and irrigated fields. Among the drought resistance mechanisms, drought avoidance in genotypes with fibrous roots was recognized to be associated with drought resistance in soybean. Plant introduction PI416937 was shown to possess fibrous roots and has been used as a parent in breeding programs to improve soybean productivity. Little information is available on relative contribution and chromosomal location of quantitative trait loci (QTL) conditioning fibrous roots in soybean. To identify the genomic locations and genetic bases of this trait, a recombinant inbred line population was derived from a cross between PI416937 and ‘Benning’. To detect associated QTLs, phenotypic data were collected and analyzed for 2 years under rain-fed field conditions. The selective genotyping approach was used to reduce the costs and work associated with conducting the QTL analysis. A total of five QTLs were identified on chromosomes Gm01 (Satt383), Gm03 (Satt339), Gm04 (Sct_191), Gm08 (Satt429), and Gm20 (Sat_299), and together explained 51% of the variation in root score. Detected QTLs were co-localized with QTLs related to root morphology, suggesting that fibrous roots QTL may be associated with other morpho-physiological traits and seed yield in soybean. Genetic dissection of the fibrous roots trait at the individual marker loci will allow for marker-assisted selection to develop soybean genotypes with enhanced levels of fibrous roots.     

QTL in mega-environments: II. Agronomic trait QTL co-localized with seed yield QTL detected in a population derived from a cross of high-yielding adapted × high-yielding exotic soybean lines

Seed yield mega-environment-universal and specific QTL (QTL_U and QTL_SP, respectively) linked to Satt100, Satt130, Satt162, Satt194, Satt259 Satt277 and Sat_126, have been identified in a population derived from a cross between a Chinese and a Canadian soybean [Glycine max (L.) Merrill] elite line. The variation observed in yield could be the consequence of the variation of agronomic traits. Yield-component traits have been reported in the literature, but a better understanding of their impact at the molecular level is still lacking. Therefore, the objectives of this study were to identify traits correlated with yield and to determine if the yield QTL_U and QTL_SP were co-localized with QTL_U and QTL_SP associated with an agronomic trait. A recombinant inbred line (RIL) population was developed from a cross between a high-yielding adapted Canadian and a high-yielding exotic Chinese soybean elite line. The RIL were evaluated in multiple environments in China and Canada during the period from 2004 to 2006. Four yield QTL_U, tagged by markers Satt100, Satt277, Satt162 and Sat_126, were co-localized with a QTL associated with an agronomic trait, behaving as either QTL_U or QTL_SP for the agronomic trait. For example, the yield QTL_U, tagged by marker Satt100 was associated also with 100 seed weight, pods per plant, pods per node, plant height, R1, R5, R8, oil content and protein content in all Canadian environments, but only with pods per plant, pods per node, plant height, R1, R5, R8 and oil content in two or more Chinese environments. No agronomic traits QTL were co-localized with the yield QTL_U tagged by the marker Satt139 or the yield QTL_SP tagged by Satt259, suggesting a physiological basis of the yield in these QTL. The results suggest that a successful introgression of crop productivity alleles from plant introductions into an adapted germplasm could be facilitated by the use of both the QTL_U and QTL_SP because each type of QTL contributed either directly or indirectly through yield-component traits to seed yield of RILs.     

Genomic Regions Associated with Amino Acid Composition in Soybean

Soybean [Glycine max (L.) Merr.] is the single largest source of protein in animal feed. However, few studies have been conducted to evaluate genomic regions controlling amino acid composition in soybean. It is important to study the genetics of amino acid composition to achieve improvements through breeding. The objectives of this study were to determine the ratios between essential to non-essential (E:NE) and essential to total (E:T) amino acids, and to identify genomic regions controlling essential and non-essential amino acid composition in soybean seed. To achieve these objectives, 101 F₆-derived recombinant inbred lines (RIL) developed from a cross of N87-984-16 × TN93-99 were used. Ground soybean seed samples were analyzed for amino acids using a near infrared spectroscopy (NIRS) instrument. A significant (p < 0.01) difference among the RIL was found for amino acid composition. Heritability estimates on an entry mean basis ranged from 0.13 for His to 0.67 for Tyr. A total of 94 polymorphic simple sequence repeat (SSR) molecular genetic markers were screened in DNA from progenies. Single factor ANOVA was used to identify candidate quantitative trait loci (QTL), which were then confirmed by QTL Cartographer. At least one QTL for each amino acid was detected in this population. QTL linked to molecular markers Satt143, Satt168, Satt203, Satt274 and Satt495 were associated with most of the amino acids. Phenotypic variation explained by an individual QTL ranged from 9.4 to 45.3%. QTL detected for amino acids in soybean in this experiment are expected to be useful for future breeding programs targeting development of improved soybean amino acid composition for human and animal nutrition.     

Pyramided QTL underlying tolerance to Phytophthora root rot in mega-environments from soybean cultivars ‘Conrad’ and ‘Hefeng 25’

Phytophthora root rot (PRR) of soybean (Glycine max (L.) Merr.) is the second most important cause of yield loss by disease in North America, surpassed only by soybean cyst nematode (Wrather et al. in Can J Plant Pathol 23:115–121, 2001). Tolerance can provide economically useful disease control, conditioning partial resistance of soybean to PRR. The aims of this study were to identify new quantitative trait loci (QTL) underlying tolerance to PRR, and to evaluate the effects of pyramided or stacked loci on the level of tolerance. A North American cultivar ‘Conrad’ (tolerant to PRR) was crossed with a northeastern China cultivar ‘Hefeng 25’ (tolerant to PRR). Through single-seed descent, 140 F_2:5 and F_2:6 recombinant inbred lines were advanced. A total of 164 simple sequence repeat (SSR) markers were used to construct a genetic linkage map. The percentage of seedling death was measured over 2 years (2007 and 2008) in the field at four naturally infested locations in Canada and China following additional soil infestation and in the greenhouse following inoculation with Phytophthora sojae isolate. A total of eight QTL underlying tolerance to PRR were identified, located in five linkage groups (F, D1b+w, A2, B1, and C2). The phenotypic variation contributed by the loci ranged from 4.24 to 27.98%. QPRR-1 (anchored in the interval of SSR markers Satt325 and Satt343 of LG F), QPRR-2 (anchored in the interval of Satt005 and Satt600 of LG D1b+w), and QPRR-3 (anchored in the interval of Satt579 and Sat_089 of LG D1b+w) derived their beneficial allele from ‘Conrad’. They were located at chromosomal locations known to underlie PRR tolerance in diverse germplasm. Five QTL that derived beneficial alleles from ‘Hefeng 25’ were identified. The QTL (QPRR-1 to QPRR-7) that were detected across at least three environments were selected for loci stacking and to analyze the relationship between number of tolerance loci and disease loss percentage. The accumulation of tolerance loci was positively correlated with decreases in disease loss percentage. The pyramid of loci underlying tolerance to PRR provided germplasm useful for crop improvement by marker-assisted selection and may provide durable cultivar tolerance against the PRR disease.     

Identification of QTLs Underlying Water-Logging Tolerance in Soybean

Soil water-logging can cause severe damage to soybean [Glycine max (L.) Merr.] and results in significant yield reduction. The objective of this study was to identify quantitative trait loci (QTL) that condition water-logging tolerance (WLT) in soybean. Two populations with 103 and 67 F_6:11 recombinant inbred lines (RILs) from A5403 × Archer (Population 1) and P9641 × Archer (Population 2), respectively, were used as the mapping populations. The populations were evaluated for WLT in manually flooded fields in 2001, 2002, and 2003. Significant variation was observed for WLT among the lines in the two populations. No transgressive tolerant segregants were observed in either population. Broad-sense heritability of WLT for populations 1 and 2 were 0.59 and 0.43, respectively. The tolerant and sensitive RILs from each population were selected to create a tolerant bulk and a sensitive bulk, respectively. The two bulks and the parents of each population were tested with 912 simple sequence repeat (SSR) markers to select candidate regions on the linkage map that were associated with WLT. Markers from the candidate regions were used to genotype the RILs in both populations. Both single marker analysis (SMA) and composite interval mapping (CIM) were used to identify QTL for WLT. Seventeen markers in Population 1 and 15 markers in Population 2 were significantly (p <0.0001) associated with WLT in SMA. Many of these markers were linked to Rps genes or QTL conferring resistance to Phytophthora sojae Kaufmann and Gerdemann. Five markers, Satt599 on linkage group (LG) A1, Satt160, Satt269, and Satt252 on LG F, and Satt485 on LG N, were significant (p <0.0001) for WLT in both populations. With CIM, a WLT QTL was found close to the marker Satt385 on LG A1 in Population 1 in 2003. This QTL explained 10% of the phenotypic variation and the allele that increased WLT came from Archer. In Population 2 in 2002, a WLT QTL was located near the marker Satt269 on LG F. This QTL explained 16% of the phenotypic variation and the allele that increased WLT also came from Archer.     

QTL in mega-environments: I. Universal and specific seed yield QTL detected in a population derived from a cross of high-yielding adapted × high-yielding exotic soybean lines

Modern soybean [(Glycine max (L.) Merrill] breeding programs rely primarily on the use of elite × elite line crosses to develop high-yielding cultivars. Favorable alleles for traits of interest have been found in exotic germplasm but the successful introduction of such alleles has been hampered by the lack of adaptation of the exotic parent to local mega-environment and difficulties in identifying superior progeny from elite × exotic crosses. The objective of this study was to use a population derived from a cross between an adapted and an exotic elite line to understand the genetic causes underlying adaptation to two mega-environments (China and Canada). A cross between a high-yielding Canadian cultivar ‘OAC Millennium’ and an elite Chinese cultivar ‘Heinong 38’ was performed to develop a recombinant inbred line (RIL) population. The RIL population was evaluated in China and Canada in multiple environments from 2004 to 2006. Significant variation for seed yield was observed among the RILs in both the Chinese and Canadian environment. Individual RILs performed differently between the Chinese and Canadian environments suggesting differential adaptation to intercontinental mega-environments. Seven seed yield quantitative trait loci (QTL) were identified of which five were mega-environment universal QTL (linked to markers Satt100, Satt162, Satt277, Sat_126, and the interval of Satt139-Sat_042) and two were mega-environment-specific QTL (at marker intervals, Satt194-SOYGPA and Satt259-Satt576). Seed yield QTL located near Satt277 has been confirmed and new QTL have been identified explaining between 9 and 37% of the phenotypic variation in seed yield. The QTL located near Satt100 explained the greatest amount of variation ranging from 18 to 37% per environment. Broad sense heritability ranged from 89 to 64% among environments. Epistatic effects have been identified in both mega-environments with pairs of markers explaining between 9 and 14% of the phenotypic variation in seed yield. An improved understanding of the type of QTL action as either universal or mega-environment-specific QTL as well as their interaction may facilitate the development of strategies to introgress specific high-yielding alleles from Chinese to North American germplasm and vice versa to sustain efforts in breeding of high-yielding soybean cultivars.     

Identification of a new major QTL associated with resistance to soybean cyst nematode (Heterodera glycines)

Resistance of soybean [Glycine max (L.) Merr.] to cyst nematode (SCN) (Heterodera glycines Ichinohe), one of the most destructive pathogens affecting soybean, involves a complex genetic system. The identification of QTLs associated with SCN resistance may contribute to the understanding of such system. The objective of this work was to identify and map QTLs for resistance to SCN Race 14 with the aid of molecular markers. BC₃F_2:3 and F_2:3 populations, both derived from an original cross between resistant cv. Hartwig and the susceptible line BR-92–31983 were screened for resistance to SCN Race 14. Four microsatellite (Satt082, Sat_001, Satt574 and Satt301) and four RAPD markers (OPAA-11₇₉₅, OPAE-08₈₃₇, OPR-07₅₄₈ and OPY-07₂₀₃₀) were identified in the BC₃F_2:3 population using the bulked segregant analysis (BSA) technique. These markers were amplified in 183 F_2:3 families and mapped to a locus that accounts for more than 40% of the resistance to SCN Race 14. Selection efficiency based on these markers was similar to that obtained with the conventional method. In the case of the microsalellite markers, which identify homozygous resistant genotypes, the efficiency was even higher. This new QTL has been mapped to the soybean linkage group D2 and, in conjunction with other QTLs already identified for SCN resistance, will certainly contribute to our understanding of the genetic basis of resistance of this important disease in soybean. Received: 12 October 1999 / Accepted: 14 April 2000     

An informative set of SSLP markers and genomic profiles in the rat MHC,the <Emphasis Type="Italic">RT1</Emphasis> complex

Almost 10,000 single nucleotide polymorphisms (SNPs) had been identified in the RT1 complex, the major histocompatibility complex of the rat, but less than ∼0.5% have been characterized. In the context of the incomplete characterization of most SNPs, simple sequence length polymorphism (SSLP) marker development is still valuable for understanding the involvement of genes in the RT1 in controlling disease susceptibility, since SSLPs are user-friendly and cost-effective genetic markers in rat genome analysis. In this study, we developed a set of 67 SSLP markers, including 57 novel markers, to cover the entire RT1 complex and then created genetic profiles across 67 rat strains. These markers are located almost every 50 kb in the RT1 complex and show comparable polymorphism; the average number of alleles was 8.04 ± 3.44 and the average polymorphic rate was 71 ± 23%. Interestingly, markers failing to amplify polymerase chain reaction products were highly observed in all strains except for BN/SsNHsd, which suggests the existence of highly variable genomic sequences or genomic rearrangements in the RT1 region across rat strains. Based on the phylogenic tree and individual genotyping data, we identified 28 SSLP marker haplotypes in the RT1 region that roughly consisted of three genomic regions. These findings provided new insight into the genomic organization of the RT1 complex and we recognized the need of additional RT1 genome sequences in different strains. Owing to the accuracy and ease of determination, PCR-based SSLP genotyping could replace serological typing in genetic analyses and characterization of rat major histocompatibility. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

Linkage Mapping of DNA Markers Generated with Specific and Non-Specific Gene Primers in Soybean

Polymerase chain reaction (PCR) has been used extensively in the construction of linkage maps for many cultivated crops including soybean, [Glycine max (L.) Merr]. In this study, four sets of oligonucleotide primer pairs of known genes (pearl millet Adh 1, nodule specific proline-rich protein, Drosophila homeobox, heat shock protein), several different combinations from kits A, D, E, and J of arbitrary primers and five primer pairs of soybean simple sequence repeats of varying length (Satt 9, Satt 20, Satt 42, Satt 64, and Satt 30) were utilized in PCR to identify molecular markers which were then used to construct a genetic linkage map. DNA for the PCR reactions was isolated from 65 recombinant inbred soybean lines resulting from crossing PI 290,136 and BARC-2 (Rj ₄ ), followed by self-pollination for seven generations without selection. Mapmaker 3.0, a computer package, was used for construction of the linkage map. A total of 43 polymorphic markers were identified; 30 markers were linked and distributed among 5 linkage groups while 13 markers were unlinked. Arbitrary primers revealed more polymorphisms than specific primers. A combination of arbitrary primers A5 and A18 revealed the maximum number of polymorphic bands. Five observed linkage groups can be expanded in future soybean research by using additional markers.     

A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene

 We constructed a bacterial artificial chromosome (BAC) library for soybean (Glycine max) consisting of approximately 30 000 clones with an average insert size of 120 kilobase pairs. The library was successfully screened with restriction fragment length polymorphism (RFLP) and microsatellite markers tightly linked to a major resistance gene for the cyst nematode, Heterodera glycines. Since many soybean RFLPs hybridize to duplicate loci, BACs homologous to duplicate RFLP loci were distinguished by digestion with the restriction enzyme originally used to map the RFLP, followed by a comparison of the hybridizing fragments. Linkage mapping of BAC clones identified with markers linked to the cyst nematode resistance gene demonstrated that these clones were located at the expected chromosomal positions and that there were no indications of chimeras within the genomic inserts. Received: 3 July 1997/Accepted: 26 August 1997     

Molecular mapping of pea powdery mildew resistance gene <Emphasis Type="Italic">er2</Emphasis> to pea linkage group III

Powdery mildew caused by Erysiphe pisi D.C. is one of the most serious diseases that inflict heavy losses to pea crop world-wide. Identification of resistance sources and their incorporation into susceptible cultivars remains the most effective method of controlling the disease. The present study investigated the resistance phenotype, inheritance, and genomic location of gene(s) controlling resistance to powdery mildew in pea genotype ‘JI2480’. The powdery mildew resistance in ‘JI2480’ appeared to be a spatial phenomenon showing expression only in leaf tissues. By segregation analysis of an F₂ progeny of cross ‘Lincoln/JI2480’, the leaf resistance of ‘JI2480’ was shown to be controlled by a single recessive gene, presumed to be er2. Through linkage analysis of 111 resistant F₂ progeny plants with simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) markers adopted from the published linkage maps, the er2 gene was localized on pea linkage group III (LGIII). The assignment of er2 to LGIII, a position different from that reported for er1, has resolved the long standing controversy in the literature regarding the existence and genomic location of er2 gene. A RAPD marker OPX-17_1400, exhibiting cis phase linkage (2.6 cM) to er2 was successfully converted to a sequence characterized amplified region (SCAR) marker, ScX17_1400. The SCAR marker ScX17_1400 will ensure speedy and precise introgression of er2 into susceptible cultivars by permitting selection of er2 heterozygotes amongst BC _n F₁s without progeny tests and resistance screening.     

Genomic selection in forest tree breeding

Genomic selection (GS) involves selection decisions based on genomic breeding values estimated as the sum of the effects of genome-wide markers capturing most quantitative trait loci (QTL) for the target trait(s). GS is revolutionizing breeding practice in domestic animals. The same approach and concepts can be readily applied to forest tree breeding where long generation times and late expressing complex traits are also a challenge. GS in forest trees would have additional advantages: large training populations can be easily assembled and accurately phenotyped for several traits, and the extent of linkage disequilibrium (LD) can be high in elite populations with small effective population size (N _e) frequently used in advanced forest tree breeding programs. Deterministic equations were used to assess the impact of LD (modeled by N _e and intermarker distance), the size of the training set, trait heritability, and the number of QTL on the predicted accuracy of GS. Results indicate that GS has the potential to radically improve the efficiency of tree breeding. The benchmark accuracy of conventional BLUP selection is reached by GS even at a marker density ~2 markers/cM when N _e ≤ 30, while up to 20 markers/cM are necessary for larger N _e. Shortening the breeding cycle by 50% with GS provides an increase ≥100% in selection efficiency. With the rapid technological advances and declining costs of genotyping, our cautiously optimistic outlook is that GS has great potential to accelerate tree breeding. However, further simulation studies and proof-of-concept experiments of GS are needed before recommending it for operational implementation.     

Use of allele specificity of comigrating AFLP markers to align genetic maps from different potato genotypes

The allele specificity of AFLP markers was assessed in five relatively unrelated potato genotypes. To this end, two diploid mapping populations of potato, F₁SH × RH and F₁AM × RH, were analysed using four and six AFLP primer combinations, respectively, recently applied to the analysis of the genetically well characterized backcross population BC_C × E. The AFLP profiles of the five parents revealed 733 AFLP markers and, when identical primer combinations were used, 131 comigrating AFLP markers were identified. After construction of five parental maps, the genomic positions of these comigrating AFLP markers were compared and 117 markers (89%) which targeted the same genomic region were assumed to be homologous. Of these putative homologues, 20 markers, each cloned from at least two genotypes, were sequenced and 19 sets of amplification products were shown to be nearly identical. The number of AFLP markers previously mapped in population BC_C × E ranged from three to eleven per chromosome, which allowed a reliable assessment of chromosome numbers from individual linkage groups obtained in populations F₁SH × RH and F₁AM × RH. The high incidence of corresponding AFLP alleles was confirmed by using an additional set of five primer combinations. The 733 AFLP markers localized provide a valuable reference collection for future mapping studies in potato. As a consequence AFLP analysis may replace more laborious locus-specific marker techniques. Received: 26 July 1996 / Accepted: 30 January 1997