Mapping and identification of QTLs for seed fatty acids in soybean(Glycine max L.)

Soybean is one of the most important sources of vegetable oil.The oil content and fatty acid ratio have attracted significant attention due to their impacts on the shelf-life of soybean oil products and consumer health.In this study,a high-density genetic map derived from Guizao 1 and Brazil 13 was used to analyze the quantitative trait loci of palmitic acid(PA),stearic acid(SA),oleic acid(OA),linoleic acid(LA),linolenic acid(LNA),and oil content(OC).A total of 54 stable QTLs were detected in the genetic map linkage analysis,which shared six bin intervals.Among them,the bin interval on chromosome 13(bin106-bin118 and bin123-bin125)was found to include stable QTLs in multiple environments that were linked to OA,LA,and LNA.Eight differentially expressed genes(DEGs)within these QTL intervals were determined as candidate genes according to the combination of parental resequencing,bioinformatics and RNA sequencing data.All these results are conducive to breeding soybean with the ideal fatty acid ratio for food,and provide the genetic basis for mining genes related to the fatty acid and oil content traits in soybean.

A novel procedure for identifying a hybrid QTL-allele system for hybrid-vigor improvement, with a case study in soybean(Glycine max)yield

“Breeding by design” for pure lines may be achieved by construction of an additive QTL-allele matrix in a germplasm panel or breeding population, but this option is not available for hybrids, where both additive and dominance QTL-allele matrices must be constructed. In this study, a hybrid-QTL identification approach, designated PLSRGA, using partial least squares regression(PLSR) for model fitting integrated with a genetic algorithm(GA) for variable selection based on a multi-locus, multi-allele model is described for additive and dominance QTL-allele detection in a diallel hybrid population(DHP). The PLSRGA was shown by simulation experiments to be superior to single-marker analysis and was then used for QTL-allele identification in a soybean DPH yield experiment with eight parents. Twenty-eight main-effect QTL with 138 alleles and nine QTL × environment QTL with 46 alleles were identified, with respective contributions of 61.8% and 23.5% of phenotypic variation. Main-effect additive and dominance QTL-allele matrices were established as a compact form of the DHP genetic structure. The mechanism of heterosis superior-to-parents(or superior-to-parents heterosis, SPH) was explored and might be explained by a complementary locus-set composed of OD+(showing positive over-dominance, most often), PD+(showing positive partial-to-complete dominance, less often) and HA+(showing positive homozygous additivity, occasionally) loci, depending on the parental materials. Any locus-type, whether OD+, PD + and HA+, could be the best genotype of a locus. All hybrids showed various numbers of better or best genotypes at many but not necessarily all loci, indicating further SPH improvement. Based on the additive/dominance QTL-allele matrices, the best hybrid genotype was predicted, and a hybrid improvement approach is suggested. PLSRGA is powerful for hybrid QTL-allele detection and cross-SPH improvement.

Analysis of QTLs for the Trichome Density on the Upper and Downer Surface of Leaf Blade in Soybean [Glycine max (L.) Merr.]

Trichomes （plant hairs） are present on nearly all land plants and are known to play important roles in plant protection, specifically against insect herbivory, drought, and UV radiation. The identification of quantitative trait loci （QTL） associated with trichome density should help to interpret the molecular genetic mechanism of soybean trichome density. 184 recombinant inbred lines （RILs）, derived from a cross between soybean cultivars Kefeng 1 and Nannong 1138-2 were used as segregating population for evaluation of TDU （trichome density on the upper surface of leaf blade） and TDD （trichome density on the downer surface of leaf blade）. A total of 15 QTL were detected on molecular linkage groups （MLG） A2, Dla, Dlb, E and H by composite interval mapping （CIM） and among all the QTL, qtuA2-1, qtuD 1 a-1, qtuD lb-2, qtuH-2 qtuE-1, qtdDlb-2, and qtdH- 2 were affirmed by multiple interval mapping （MIM）. The contribution ofphenotypic variance of qtuH-2 was 31.81 and 29.4% by CIM and MIM, respectively, suggesting it might be major gene Ps loci. Only 10 pairs of main QTL interactions for TDU were detected, explained a range of 0.2-5.1% of phenotypic variations for each pair for a total of 22.8%. The QTL on MLG Dlb affecting trichome density were mapped near to Rsc-7 conditioning resistance to SMV （soybean mosaic virus）. This study showed that the genetic mechanism of trichome density was the mixed major gene and polygene inheritance, and also suggested that the causal nature between trichome density and other agronomic traits.

Genome-wide association with transcriptomics reveals a shade-tolerance gene network in soybean

Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance.An improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with both.Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages.From the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network.Altogether,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.

Searching for plant NLR immune receptors conferring resistance to potyviruses

To fight against invasion by pathogens,plants have evolved an elaborate innate immune system,of which the nucleotide-binding domain leucine-rich repeat-containing receptor(NLR)acts as the sensor and immune executor.Potyviruses,comprising one of the largest genera of plant viruses,cause severe crop yield losses worldwide.Inherited crop resistance to potyviruses can be used in breeding and plant transgenesis to control disease development.This review summarizes achievements in mapping and cloning NLR genes conferring dominant resistance against potyvirus in the families Fabaceae,Solanaceae,Brassicaceae,and Cucurbitaceae.It compares mechanisms of potyviral protein recognition and downstream signaling employed by NLRs and discusses strategies for exploiting NLRs to better control diseases caused by potyviruses.

Maize-soybean strip intercropping： Achieved a balance between high productivity and sustainability

Intercropping is one of the most vital practice to improve land utilization rate in China that has limited arable land resource. However, the traditional intercropping systems have many disadvantages including illogical field lay-out of crops, low economic value, and labor deficiency, which cannot balance the crop production and agricultural sustainability. In view of this, we developed a novel soybean strip intercropping model using maize as the partner, the regular maize-soybean strip intercropping mainly popularized in northern China and maize-soybean relay-strip intercropping principally extended in southwestern China. Compared to the traditional maize-soybean intercropping systems, the main innovation of field lay-out style in our present intercropping systems is that the distance of two adjacent maize rows are shrunk as a narrow strip, and a strip called wide strip between two adjacent narrow strips is expanded reserving for the growth of two or three rows of soybean plants. The distance between outer rows of maize and soybean strips are expanded enough for light use efficiency improvement and tractors working in the soybean strips. Importantly, optimal cultivar screening and increase of plant density achieved a high yield of both the two crops in the intercropping systems and increased land equivalent ratio as high as 2.2. Annually alternative rotation of the adjacent maize-and soybean-strips increased the grain yield of next seasonal maize, improved the absorption of nitrogen, phosphorus, and potasium of maize, while prevented the continuous cropping obstacles. Extra soybean production was obtained without affecting maize yield in our strip intercropping systems, which balanced the high crop production and agricultural sustainability.

Fine Mapping and Candidate Gene Analysis of Resistance Gene R_(SC3Q) to Soybean mosaic virus in Qihuang 1

Soybean mosaic virus （SMV） disease is one of the most destructive viral diseases in soybean （Glycine max （L.） Merr.）. SMV strain SC3 is the major prevalent strain in huang-huai and Yangtze valleys, China. The soybean cultivar Qihuang 1 is of a rich resistance spectrum and has a wide range of application in breeding programs in China. In this study, F1, F2 and F2：3 from Qihuang 1×nannong 1138-2 were used to study inheritance and linkage mapping of the SC3 resistance gene in Qihuang 1. The secondary F2 population and near isogenic lines （nILs） derived from residual heterozygous lines （RhLs） of Qihuang 1×nannong 1138-2 were separatively used in the ifne mapping and candidate gene analysis of the resistance gene. Results indicated that a single dominant gene （designated RSC3Q） controls resistance, which was located on chromosome 13. Two genomic-simple sequence repeat （SSR） markers BARCSOYSSR_13_1114 and BARCSOYSSR_13_1136 were found lfanking the two sides of the RSC3Q. The interval between the two markers was 651 kb. Quantitative real-time PCR analysis of the candidate genes showed that ifve genes （Glyma13g25730, 25750, 25950, 25970 and 26000） were likely involved in soybean SMV resistance. These results would have utility in cloning of RSC3Q resistance candidate gene and marker-assisted selection （MaS） in resistance breeding to SMV.

Identification, Genetic Analysis and Mapping of Resistance to Phytophthora sojae of Pm28 in Soybean

Phytophthora sojae Kanfman and Gerdemann （P. sojae） is one of the most prevalent pathogens and causes Phytophthora root rot, which limits soybean production worldwide. Development of resistant cultivars is a cost-effective approach to controlling this disease. In this study, 127 soybean germplasm were evaluated for their responses to Phytophthora sojae strain Pm28 using the hypocotyl inoculation technique, and 49 were found resistant to the strain. The hypocotyl of P1, P2, F1, and F2：3 of two crosses of Ludou 4 （resistant）×Youchu 4 （susceptible） and Cangdou 5 （resistant）×Williams （susceptible） were inoculated with Pm28, and were used to analyze the inheritance of resistance. The population derived from the cross of Ludou 4×Youchu 4 was used to map the resistance gene （designated as Rps9） to a linkage group. 932 pairs of SSR primers were used to detect polymorphism, and seven SSR markers were mapped near the resistance gene. The results showed that the resistance to Pm28 in Ludou 4 and Cangdou 5 was controlled by a single dominant gene Rps9, which was located on the molecular linkage group N between the SSR markers Satt631 （7.5 cM） and Sat_186 （4.3 cM）.

Marker-assisted pyramiding of soybean resistance genes R_(SC4),R_(SC8),and R_(SC14Q) to soybean mosaic virus

Soybean mosaic virus （SMV） is one of the major viral pathogens affecting soybean crops worldwide. Three SMV resistance genes, Rsc4, Rsc8, and Rsc14Q, have been identified and mapped on soybean chromosomes 14, 2, and 13 from Dabaima, Kefeng 1, and Qihuang 1 cultivars, respectively. Soybean cultivar Nannong 1138-2 is widely grown in the Yangtze River Valley of China. In this study, crosses were made between Qihuang l^Kefeng 1 and DabaimaxNannong 1138-2. Ten simple sequence repeat （SSR） markers linked to three resistance loci （Rsc4, Rsc8, and Rsc^4Q） were used to assist pyramided breeding. Pyramided families containing three resistance loci （Rsc4, Rsc8, and Rsc14Q） were evaluated by inoculating them with 21 SMV strains from China. Results indicated that the 10 markers can be used effectively to assist the selection of resistant individuals containing Rsc4, Rsc8, and Rsc14Q. A total of 53 F6 plants were confirmed to contain three homozygous alleles conferring resistance to SMV. Five F7 homozygous pyramided families exhibited resistance to 21 strains of SMV and showed desirable agronomic traits using dual selection. The strategy of pyramiding resistance gene derived from different varieties has practical breeding value in providing broad-spectrum resistance against the existing strains of SMV in China.

Cloning and Characterization of a Novel Gene GmMF1 in Soybean (Glycine max L. Merr.)

Cytoplasmic male sterility plays an important role in utilization of crop heterosis. Screening of soybean for novel genes related to male sterility in soybean could provide a basis for studying the molecular mechanism of male sterility in plants. In this study, gene differential expressions between the cytoplasmic male-sterile line NJCMS 1A and its maintainer line NJCMS 1B in soybean were analyzed using cDNA-AFLP. A differentially expressed fragment, GmMF-T4A15, was isolated from large flower buds of NJCMS1B. By searching the soybean genomic library and PCR amplification, the cDNA fulllength sequence of 1 311 bp was obtained and named GmMF1. The expression characteristics of GmMF1 were studied by semiquantitative real-time PCR and real-time quantitative PCR. The results showed that GmMF1 was expressed highly in flower buds of NJCMS1B. The deduced protein contains 436 amino acids and shows high similarity to members of the DUF620 protein family with unknown functions in other plant species. It is predicted that the protein encoded by GmMF1 is localized in the nucleus.

Sampling Survey and Identification of Races of Soybean Cyst Nematode (Heterodera glycines Ichinohe) in Huang-Huai Valleys

Soybean cyst nematode （SCN Heterodera glycines Ichinohe） is one of the most important nationwide soybean diseases in China. A total of 38 soil specimens or locations in the area was sampled and tested for SCN races during 2001-2003 for the inspection of race distribution in Huang-Huai Valleys. A map of race distribution was constructed according to the data from both the present study and the published reports cited. Three areas, namely, the area of southeast to Jinan in Shangdong Province; the area of northern Henan Province and its border region to south of Hebei Province; and the area of Luohe, Zhoukou of Henan Province and Fuyang of Anhui Province mainly infested with Race 1 were identified. Race 4 was predominant in Shanxi Province, Beijing and the adjacent area of Henan, Shandong, and Anhui provinces, and the delta of Huanghe River in Shandong Province. Race 2 was mainly found in Liaocheng, Dezhou of Shangdong Province and Shijiazhuang of Hebei Province, and Jiaozuo and Huojia of Henan Province. Race 7 was distributed in the west part of Jiaodong Peninsula of Shandong Province and Kaifeng, Huaxian, Wenxian of Henan Province. Race 5 was found and scattered in Hebei and Henan Province. Race 9 was found in Shangqiu of Henan Province, which was reported for the first time in China. It can be seen that Race 1 and Race 4 were the two predominant races in Huang-Huai Valleys, and that research should focus on developing resistant cultivars of these races. There might exist other races in an area with some predominant races. The race substitution in the past decade was not obviously found, therefore, the results should be meaningful to future breeding for resistance to SCN in Huang-Huai Valleys.

A MADS-box gene is involved in soybean resistance to multiple Soybean mosaic virus strains

Soybean mosaic virus(SMV)is a member of the genus Potyvirus that extensively impairs global soybean production.The full-length coding sequence of the MADS-box transcription factor Gm CAL was cloned from the SMV-resistant soybean cultivar Kefeng 1.SMV-induced expression analysis indicated that Gm CAL responded quickly to SMV-SC8 infection in Kefeng 1 but not in NN1138-2.Gm CAL was expressed at high levels in flowers and pods but at lower levels in leaves.The gene was localized to the nucleus by subcellular localization assay.Virus-induced gene silencing did not increase the accumulation of SMV in Gm CAL-silenced Kefeng 1 plants(with silencing efficiency~80%)after SC8 inoculation.Gm CAL-silencing plants still conferred resistance to SC8 that might be owing to incomplete silencing of genes with lower expression.SMV content decreased significantly in Gm CAL-overexpressing NN1138-2 plants after SMVSC3,SMV-SC7,and SMV-SC8 inoculation in comparison with a vector control,showing that overexpression of Gm CAL conferred broad-spectrum resistance to multiple SMV strains.These results confirm that Gm CAL,a key regulator but not a specific SC8 resistance gene(Rsc8),is a positive regulatory transcription factor involved in soybean resistance to SMV.

A novel TIR-NBS-LRR gene regulates immune response to Phytophthora root rot in soybean

Phytophthora root rot(PRR),caused by Phytophthora sojae,is a devastating disease of soybean.The NBSLRR gene family is a class of plant genes involved in disease resistance.miRNA mediates plant response to biotic stresses by regulating the expression of target genes at the transcriptional or post-translational level.Glyma.16G135500,encoding an NBS-LRR-type protein,is a target of gma-miR1510 that responds to pathogen infections.We cloned and overexpressed Glyma.16G135500(naming it GmTNL16)and knocked down mi R1510 using short tandem target mimic technology to identify the roles of the GmTNL16/gma-mi R1510 pair in the interaction of soybean and the oomycete.By overexpressing GmTNL16 in transgenic hairy roots of soybean,we showed that biomass of P.sojae was lower in overexpressing hairy roots than in control roots.Thus,miR1510 expression was reduced upon P.sojae infection,reflecting the induced expression of GmTNL16 conferring resistance to P.sojae in soybean.Differentially expressed genes were enriched in plant-pathogen interaction,plant hormone signal transduction,and secondary metabolism by RNA sequencing analyze.In particular,jasmonate and salicylic acid pathway-associated genes,including JAZ,COI1,TGA,and PR,responded to P.sojae infection.All of these results indicate that the GmTNL16/gma-miR1510 pair participates in soybean defense response via the JA and SA pathways.

Two soybean homologues of TERMINAL FLOWER 1 control flowering time under long day conditions

Flowering time is a key agronomic trait that directly affect the adaptation and yield of soybean.After whole genome duplications,about 75%of genes being represented by multiple copies in soybean.There are four TERMINAL FLOWER 1(TFL1)genes in soybean,and the TFL1b(Dt1)has been characterized as the determinant of stem growth habit.The function of other TFL1 homologs in soybean is still unclear.Here,we generated knockout mutants by CRISPR/Cas9 genome editing technology and found that the tfl1c/tfl1d double mutants flowered significantly earlier than wild-type plants.We investigated that TFL1c and TFL1d could physically interact with the b ZIP transcription factor FDc1 and bind to the promoter of APETALA1a(AP1a).RNA-seq and q RT-PCR analyses indicated that TFL1c and TFL1d repressed the expressions of the four AP1 homologs and delayed the flowering time in soybean.The two genes play important roles in the regulation of flowering time in soybean and mainly act as the flowering inhibitors under long-day conditions.Our results identify novel components in the flowering-time regulation network of soybean and will be invaluable for molecular breeding of improved soybean yield.

Detecting the QTL-allele system controlling seed-flooding tolerance in a nested association mapping population of soybean

Soil flooding stress,including seed-flooding,is a key issue in soybean production in highrainfall and poorly drained areas.A nested association mapping(NAM)population comprising 230 lines of two recombinant inbred line(RIL)populations with a common parent was established and tested for seed-flooding tolerance using relative seedling length as indicator in two environments.The population was genotyped using RAD-seq(restriction site-associated DNA sequencing)to generate 6137 SNPLDB(SNP linkage disequilibrium block)markers.Using RTM-GWAS(restricted two-stage multi-locus multiallele genome-wide association study),26 main-effect QTL with 63 alleles and 12 QEI(QTL×environment)QTL with 27 alleles in a total of 33 QTL with 78 alleles(12 dual-effect alleles)were identified,explaining respectively 50.95%and 14.79%of phenotypic variation.The QTL-alleles were organized into main-effect and QEI matrices to show the genetic architecture of seed-flooding tolerance of the three parents and the NAM population.From the main-effect matrix,the best genotype was predicted to have genotypic value 1.924,compared to the parental value range 0.652–1.069,and 33 candidate genes involved in six biological processes were identified and confirmed byχ2 test.The results may provide a way to match the breeding by design strategy.

QTL-allele matrix detected from RTM-GWAS is a powerful tool for studies in genetics, evolution, and breeding by design of crops

The plant germplasm resources harboring abundant genetic variations are necessary wealth in developing new cultivars adapted to various geographic and seasonal conditions.Unraveling the complex genetic architecture underlying phenotypic diversity in germplasm population is essential in studies on genetics,evolution and breeding plans for crop species.Mapping quantitative trait loci(QTLs)using molecular markers provide a basic tool for understanding the inheritance of quantitative traits,while the genomewide association study(GWAS)is a potential approach to detecting the whole-genome QTLs and their corresponding alleles in a germplasm population.The previous GWAS detects QTLs by taking high-density single-nucleotide polymorphism(SNP)markers to identify genotypephenotype associations,and has been extensively used for genetic dissection of quantitative traits in plants(Huang and Han 2014).

Genetic Diversity of Chinese Soybean mosaic virus Strains and Their Relationships with Other Plant Potyviruses Based on P3 Gene Sequences

Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide （NT） sequence identities and 95.1-100% amino acid （AA） sequence identities. The P3 coding regions of the 16 SMV isolates share high identities （92.4-98.9% NT and 96.0-100% AA） with the reported Korean isolates, followed by the USA isolates （88.5-97.9% NT and 91.4-98.6% AA）, and share low identities （80.5-85.2% NT and 82.1-84.7% AA） with the reported HZ 1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus （WMV）, with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.

Molecular cloning and functional characterization of a soybean GmG MP1 gene reveals its involvement in ascorbic acid biosynthesis and multiple abiotic stress tolerance in transgenic plants

L-Ascorbic acid （AsA） plays an important role in plants and animals. In plants, GDP-D-mannose pyrophosphorylase （GMP） is essential in the AsA biosynthetic pathway. However, little is known about the genes encoding GMP in soybean and here we report genetic and functional analysis of the GmGMP1 （Glycine max GDP-D-mannose pyrophosphorylase 1） gene in this species. GmGMP1 encoded a GDP-mannose pyrophosphorylase and exhibited higher transcript levels in the leaf than in the root, stem, flower, and seed. Transcript of this gene was ubiquitous in the vegetative and reproductive organs, and was induced by abiotic stress and light. Increasing expression of GmGMP1 in Arabidopsis and soybean through an overexpressing approach caused pronounced enhancement of AsA content, and was implicated in lowering the superoxide anion radical content and lipid peroxidation levels in Arabidopsis, and conferring tolerance to osmotic and high salt stresses during seed germination. The present study represents the first systematic determination of soybean genes encoding GDP-mannose pyrophosphorylase and provides useful evidence for the functional involvement of GmGMP1 in control of AsA content and conferring tolerance to osmotic and salt stress.

Linkage and association mapping of wild soybean(Glycine soja)seeds germinating under salt stress

Salinity threatens soybean germination,growth and production.The germination stage is a key period in the life of soybean.Wild soybean contains many genes related to stress resistance that are valuable resources for the genetic improvement of soybean.To identify the genetic loci of wild soybean that are active during seed germination under salt stress,two populations,a soybean interspecific hybrid population comprising 142 lines and a natural population comprising 121 wild soybean accessions,were screened for three germination-related traits in this study.By using single-nucleotide polymorphism(SNP)markers with three salt tolerance indices,25 quantitative trait loci(QTLs),21 significant SNPs(–log_(10)(P)≥4.0)and 24 potential SNPs(3.5<–log_(10)(P)<4.0)were detected by linkage mapping and a genome-wide association study(GWAS)in two environments.The key genetic region was identified based on these SNPs and QTLs.According to the gene functional annotations of the W05 genome and salt-induced gene expression qRT-PCR analysis,GsAKR1 was selected as a candidate gene that responded to salt stress at the germination stage in the wild soybean.These results could contribute to determining the genetic networks of salt tolerance in wild soybean and will be helpful for molecular marker-assisted selection in the breeding of salt-tolerant soybean.

Gene Mapping of Brachytic Stem and Its Effect on Main Agronomic Traits in Soybean

Brachytic stem is a major trait in plant type .of soybean and its yield potential may be higher under high population when compared with normal stem. In the present investigation, 152 recombinant inbred line （RIL） families derived from the cross of Bogao （normal stem） and Nannong 94-156 （brachytic stem） were used to map genes and QTLs of three plant type traits and to identify the effects of brachytic stem on agronomic traits such as yield. The primary results indicated that brachytic stem （sb） and determinate growth habit （drl） were mapped on linkage groups B2 and L, three major QTLs related to plant height were detected and mapped on linkage group L near drl, another minor QTL was mapped near sb on linkage group B2-1. Lines with brachytic stem had shorter plant height, lower biomass, yield, harvest index and pods per plant, and essentially no differences in days to maturity and 100-seed weight when compared with normal stem lines. It was obvious that the effect of brachytic stem on yield was due to the decreased height, biomass and harvest index.