GmSTF accumulation mediated by DELLA protein GmRGAs contributes to coordinating light and gibberellin signaling to reduce plant height in soybean

Plant height influences plant architecture,lodging resistance,and yield performance.It is modulated by gibberellic acid(GA)metabolism and signaling.DELLA proteins,acting as central repressors of GA signaling,integrate various environmental and hormonal signals to regulate plant growth and development in Arabidopsis.We examined the role of two DELLA proteins,GmRGAa and GmRGAb,in soybean plant height control.Knockout of these proteins led to longer internodes and increased plant height,primarily by increasing cell elongation.GmRGAs functioned under different light conditions,including red,blue,and far-red light,to repress plant height.Interaction studies revealed that GmRGAs interacted with the blue light receptor GmCRY1b.Consistent with this,GmCRY1b partially regulated plant height via GmRGAs.Additionally,DELLA proteins were found to stabilize the protein GmSTF1/2,a key positive regulator of photomorphogenesis.This stabilization led to increased transcription of GmGA2ox-7b and subsequent reduction in plant height.This study enhances our understanding of DELLA-mediated plant height control,offering Gmrgaab mutants for soybean structure and yield optimization.

In silico curation of QTL-rich clusters and candidate gene identification for plant height of bread wheat

Many genetic loci for wheat plant height(PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or genetic verified dwarfing loci from QTL linkage analysis and genome-wide association study published from 2003 to 2022. A total of 332 QTL, 270 GWAS loci and 83 genes for PH were integrated onto chromosomes according to their locations in the IWGSC RefSeq v2.1 and 65 QTL-rich clusters(QRC) were defined. Candidate genes in each QRC were predicted based on IWGSC Annotation v2.1 and the information on functional validation of homologous genes in other species. A total of 38 candidate genes were predicted for 65 QRC including three GA2ox genes in QRC-4B-IV, QRC-5A-VIII and QRC-6A-II(Rht24) as well as GA 20-oxidase 2(TaSD1-3A) in QRC-3A-IV. These outcomes lay concrete foundations for mapbased cloning of wheat dwarfing genes and application in breeding.

DDG1 and G Protein α Subunit RGA1 Interaction Regulates Plant Height and Senescence in Rice(Oryza sativa)

Many studies have already shown that dwarfism and moderate delayed leaf senescence positively impact rice yield,but the underlying molecular mechanism of dwarfism and leaf senescence remains largely unknown.Here,using map-based cloning,we identified an allele of DEP2,DDG1,which controls plant height and leaf senescence in rice.The ddg1 mutant displayed dwarfism,short panicles,and delayed leaf senescence.Compared with the wild-type,ddg1 was insensitive to exogenous gibberellins(GA)and brassinolide(BR).DDG1 is expressed in various organs,especially in stems and panicles.Yeast two-hybrid assay,bimolecular fluorescent complementation and luciferase complementation image assay showed that DDG1 interacts with theα-subunit of the heterotrimeric G protein.Disruption of RGA1 resulted in dwarfism,short panicles,and darker-green leaves.Furthermore,we found that ddg1 and the RGA1 mutant was more sensitive to salt treatment,suggesting that DDG1 and RGA1 are involved in regulating salt stress response in rice.Our results show that DDG1/DEP2 regulates plant height and leaf senescence through interacting with RGA1.

The HD-Zip transcription factor GhHB12 represses plant height by regulating the auxin signaling in cotton

Upland cotton(Gossypium hirsutum L.)is the most important natural textile fiber crop worldwide.Plant height(PH)is a significant component of plant architecture,strongly influencing crop cultivation patterns,overall yield,and economic coefficient.However,cotton genes regulating plant height have not been fully identified.Previously,an HD-Zip gene(GhHB12)was isolated and characterized in cotton,which regulates the abiotic and biotic stress responses and the growth and development processes.In this study,we showed that GhHB12 was induced by auxin.Moreover,overexpression of GhHB12 induces the expression of HY5,ATH1,and HAT4,represses the spatial-temporal distribution,polar transport,and signaling of auxin,alters the expression of genes involved in cell wall expansion,and restrains the plant height in cotton.These results suggest a role of GhHB12 in regulating cotton plant height,which could be achieved by affecting the auxin signaling and cell wall expansion.

Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet

Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is imperative to identify and deploy the genes controlling foxtail millet plant height.In this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf genes.We performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq method.One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height determination.Among them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at 263A.Cleaved amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments.Taken together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding.

Transcriptome analysis reveals potential genes associated with plant height in rice

Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identified and described.Nonetheless,the molecular mechanism of height regulation in high-culm rice mutants has not been well studied.By using transcriptome and weighted gene co-expression network analysis(WGCNA),we identified the differentially expressed genes(DEGs)between high-culm rice mutants(MUT)and wild-type(WT)and explored the key pathways and potential candidate genes involved in PH regulation.Transcriptome analysis identified a total of 2,184 DEGs,of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage.Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction,ABC transportation,and steroid hormone biosynthesis.Among these metabolic pathways,LOC_Os05g43910 and LOC_Os01g35030 were auxin(IAA)-related genes,up-regulated in MUT and LOC_Os02g08500(LEPTO1),LOC_Os11g04720,and LOC_Os12g04500 were cytokinin(CK)-related genes,downregulated in MUT.The WGCNA identified four modules(light cyan,dark grey,grey,and pale turquoise)closely related to PH,and seven key genes were screened from these modules,of which two were up-regulated cell wallrelated genes(LOC_Os01g26174(OsWAK5),LOC_Os06g05050)in MUT,and one gibberellic acid(GA)gene(LOC_Os06g37364,OsKO2)was also up-regulated.These genes might be closely related to PH regulation.These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.

Mapping QTLs with epistatic effects and QTL×environment interactions for plant height using a doubled haploid population in cultivated wheat

Quantitative trait loci （QTLs） for plant height in wheat （Triticum aestivum L.） were studied using a set of 168 doubled haploid （DH） lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai＇an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions （QEs）. Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rhtl and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection （MAS）.

The Effects of Dwarfing Genes (Rht-B1b, Rht-D1b, and Rht8) with Different Sensitivity to GA_3 on the Coleoptile Length and Plant Height of Wheat

Understanding the effects of wheat dwarfing genes on the coleoptile length and plant height is crucial for the proper utilization of dwarfing genes in the improvement of wheat yield. Molecular marker analysis combined with pedigree information were used to classify wheat cultivars widely planted in major wheat growing regions in China into different categories based on the dwarfing genes they carried. The effects of the dwarfing genes with different sensitivity to gibberellins （GA3） on the coleoptile length and plant height were analyzed. Screening of 129 cultivars by molecular marker analysis revealed that 58 genotypes of wheat contained the dwarfing gene Rht-B1b, 24 genotypes of wheat contained Rht-D1b gene and 73 genotypes of wheat possessed Rht8 gene. In addition, among these 129 cultivars, 35 genotypes of wheat cultivars contained both Rht-B1b and Rht8 genes and 16 genotypes of wheat cultivars contained both Rht-D1b and Rht8 genes. Wheat cultivars with the dwarfing genes Rht-B1b or Rht-D1b were insensitive to GA3, while the cultivars with the dwarfing gene Rht8 were sensitive to GA3. Most of the wheat genotypes containing combination of Rht8 gene with either Rht-B1b or Rht-D1b gene were insensitive to GA3. The plant height was reduced by 24.6, 30.4, 28.2, and 32.2%, respectively, for the wheat cultivars containing Rht-B1b, Rht-D1b, Rht-B1b ＋ Rht8, and Rht-D1b ＋ Rht8 genes. The plant height was reduced by 14.3% for the wheat cultivar containing GA3-sensitive gene Rht8. The coleoptile length was shortened by 25.4, 31.3, 28.4 and 31.3%, respectively, in the wheat cultivars containing Rht-B1b, Rht-D1b, Rht-B1b ＋Rht8 and Rht-D1b ＋ Rht8 genes, while the coleoptile length was shortened only by 6.2% for the wheat cultivar containing Rht8 gene. We conclude that GA3-insensitive dwarfing genes （Rht-B1b and Rht-D1b） are not suitable for the wheat improvement in dryland because these two genes have effect on reducing both plant height and coleoptile length. In contrast, GA3- sensitive dwarfing gene （Rht8） is a relatively ideal candidate for the wheat improvement since it significantly reduces the plant height of wheat, but has less effect on the coleoptile length.

Developmental Genetics Analysis for Plant Height in indica Hybrid Rice Across Environments

The developmental genetics of plant height was analyzed from two groups of three-line indica hybrid rice at two environmental conditions based on the NCII design, using the additive-dominant developmental genetics models and the statistic methods. The results showed that the rice genotypes and environmental conditions could both affect plant height, and the effects of environment on plant height decreased gradually with plant development. Additive and dominant effects both governed the performance of plant height at all developmental stages. However, the degrees of effect varied among the rice genotypes. Moreover, the interaction between environments and genotypes also affected plant height. The genetic effects differed at most developmental stages. Furthermore, the expressJon of additive effect was more active than that of dominant effect. Conditional interaction effects with environment also influenced plant height during genetic development, especially at the eady stage. Mid-parent heterosis （HMP） increased gradually with the developmental stage of plant height, and maximized at the latest stage, whereas the heterosis over the better parent （HBP） showed small differences among the genotypes, and kept stable at the later stage, with positive numeric value. At most developmental stages, conditional HMP was positively significant, while conditional HBP was negatively significant. All above results suggest that HMP and HBP have some new expressions in all developmental periods and the levels and directions are quite different.

Characterization of the Main Effects, Epistatic Effects and Their Environmental Interactions of QTL on the Genetic Basis of Plant Height and Heading Date in Rice

Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitativetraits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interactions (QE) underlying plantheight and heading date, using a doubled-haploid ( DH) population consisting of 190 lines from the cross between anindica parent Zhenshan 97 and a japonica parent Wuyujing 2, and tested in two-year replicated field trials. A geneticlinkage map with 179 SSR (simple sequence repeat) marker loci was constructed. A mixed linear model approach wasapplied to detect QTL, digenic interactions and QEs for the two traits. In total, 20 main-effect QTLs, 9 digenic interactionsinvolving 18 loci, and 5 QTL by environment interactions were found to be responsible for the two traits. No interactionswere detected between the digenic interaction and environment. The amounts of variations explained by QTLs of maineffect were 53.9% for plant height and 57.8% for heading date, larger than that explained by epistasis and QEs. However,the epistasis and QE interactions sometimes accounted for a significant part of phenotypic variation and should not bedisregarded.

Identification of QTLs for Plant Height and Its Components by Using Single Segment Substitution Lines in Rice (Oryza sativa)

QTLs for plant height and its components on the substituted segments of fifty-two single segment substitution lines （SSSLs） in rice were identified through t-test （P〈0.001） for comparison between each SSSL and recipient parent Huajingxian 74. On the 14 substituted segments, 24 QTLs were detected, 10 for plant height, 2 for panicle length, 4 for length of the first internode from the top, 5 for length of the second internode from the top and 3 for length of the third internode from the top, respectively. All these QTLs were distributed on nine rice chromosomes except chromosomes 5, 9 and 11. The additive effect ranged from -4.08 to 3.98 cm, and the additive effect percentages varied from -19.35% to 10.43%.

Genetic dissection of the developmental behavior of plant height in rice under different water supply conditions

Plant height （PH） is one of the most important agronomic traits of rice, as it directly affects the lodging resistance and the high yield potential. Meanwhile, PH is often constrained by water supply over the entire growth period. In this study, a recombinant inbred line （RIL） derived from Xiaobaijingzi and Kongyu 131 strains grown under drought stress and with normal irrigation over 2 yr （2013 and 2014）, respectively （regarded as four environments）, was used to dissect the genetic basis of PH by developmental dynamics QTL analysis combined with QTL^environment interactions. QTLs with net effects excluding the accumulated effects were detected to explore the relationship between genexgene interactions and genexenvironment interactions in specific growth period. A total of 26 additive QTLs （A-QTLs） and 37 epistatic QTLs （E-QTLs） associated with PH were detected by unconditional and conditional mapping over seven growth periods, qPH-2-3, qPH-4-3, qPH-6-1, qPH-7-1, and qPH-12-5 could be detected by both unconditional and conditional analyses, qPH-4-3 and qPH-7-5 were detected in four stages （periods） to be sequentially expressed QTLs controlling PH continuous variation. QTLs with additive effects （A-QTLs） were mostly expressed in the period $3iS2 （the time interval from stages 2 to 3）, and QTLxenvironment interactions performed actively in the first three stages （periods） which could be an important developmental period for rice to undergo external morphogenesis during drought stress. Several QTLs showed high adaptability for drought stress and many QTLs were closely related to the environments such as qPH-3-5, qPH-2-2 and qPH-6-1. 72.5% of the QTLs with a and aa effects detected by conditional analysis were under drought stress, and the PVE of QTLs detected by conditional analysis under drought stress were also much higher than that under normal irrigation. We infer that environments would influence the detection results and sequential expression of genes was highly influenced by environments as well. Many QTLs （qPH-1-2, qPH-3-5, qPH-4-1, qPH-2-3） coincident with previously identified drought resistance genes. The result of this study is helpful to elucidating the genetic mechanism and regulatory network underlying the development of PH in rice and providing references to marker assisted selection.

QTL Analysis for Plant Height with Molecular Markers in Maize

Plant height has become one of important agronomic traits with the increase of planting density recently and the rapid developments of molecular markers have provided powerful tools to localize important agronomic QTL at the genomic level. The purposes of this investigation are to map plant height QTL with molecular markers and to analyze their genetic effects in maize. An F 2∶3 population from an elite combination (Zong3×87-1) was utilized for evaluating plant height in two locations, Wuhan and Xiangfan, with a randomized complete block design. The mapping population included 266 F 2∶3 family lines. A genetic linkage map, containing 150 SSR and 24 RFLP markers, was constructed, spanning a total of 2 531.6 cm with an average interval of 14.5 cm. Totally 10 QTL affecting plant height were mapped on six different chromosomes with the composite interval mapping. Seven of 10 QTL were detected in two locations. The contributions to phenotypic variations for the single QTL varied between 5.3 and 17.1%. Additive, partial dominance, dominance, and overdominance actions existed among all detected QTL affecting plant heights. A large number of digenic interactions for plant height were detected by two-way analyses of variance. 107 and 98 two-locus combinations were found to be significant at a 0.01 probability level in two locations respectively. 23 of them were simultaneously detected in both locations. They accounted for phenotypic variations of 4.511%. It was noticed that a locus, umc1122, had digenic interactive effects with other four different loci for plant height, which distributed on three chromosomes. A few of plant height QTL was involved in significant digenic interactions, but most significant interactions occurred between markers that are not adjacent to mapped QTL. These results demonstrated that epistatic interactions might play an equal importance role as the single-locus effects in determining plant height of maize.

Quantitative trait locus mapping of yield and plant height in autotetraploid alfalfa(Medicago sativa L.)

Alfalfa(Medicago sativa L.)is the most widely grown forage legume crop worldwide.Yield and plant height are important agronomic traits influenced by genetic and environmental factors.The objective of this study was to identify quantitative trait loci(QTL)and molecular markers associated with alfalfa yield and plant height.To understand the genetic basis of these traits,a full-sib F1 population composed of 392 individuals was developed by crossing a low-yielding precocious alfalfa genotype(male parent)with a high-yielding latematuring alfalfa cultivar(female parent).The linkage maps were constructed with 3818 single-nucleotide polymorphism(SNP)markers on 64 linkage groups.QTL for yield and plant height were mapped using phenotypic data for three years.Sixteen QTL associated with yield and plant height were identified on chromosomes 1 to 8.Six QTL explained more than 10%of phenotypic variation,representing major loci controlling yield and plant height.One locus on chromosome 1 controlling yield traits had not been identified in previous studies.Three QTL co-located with other QTL(qyield-1 and qheight-7,qheight-5 and qyield-4,qheight-6,and qyield-6).With further validation,the markers closely linked with these QTL may be used for marker-assisted selection in breeding new alfalfa varieties with high yield.

A dCAPS marker developed from a stress associated protein gene TaSAP7-B governing grain size and plant height in wheat

Stress associated proteins（SAPs） are the A20/AN1 zinc-finger proteins which confer to abiotic stresses in plants. In this study, TaSAP7-B, including two AN1 domains, was isolated from B genome of wheat（Triticum aestivum L.）. Sequencing analysis on TaSAP7-B illustrated one In Del（insertion-deletion） and one SNP（single nucleotide polymorphism） in the promoter region while no diversity was observed in the coding region. On the basis of SNP in the promoter region（–260 bp）, a dCAPS（derived cleaved amplified polymorphic sequences） marker SNP-260 was developed for TaSAP7-B. Using a natural population consisting of 262 wheat accessions, significant associations were detected between the marker SNP-260 and agronomic traits, such as plant height（PH）, peduncle length（PL）, length of penultimate internode（LPI）, number of spike per plant（NSP）, and 1 000-grain weight（TGW）. Two genotypes were identified using marker SNP-260 in the natural population. Among them, the genotypes possessing C allele exhibited a higher TGW and shorter PH than the T genotypes. Hence, base C was considered as the superior allele. The dCAPS marker of TaSAP7-B can be instrumental for marker-assisted selection for high grain size and short plant height.

Heterotic loci identified for plant height and ear height using two CSSLs test populations in maize

Heterosis is an important biological phenomenon, and it has been used to increase grain yield, quality and resistance to abiotic and biotic stresses in many crops. However, the genetic mechanism of heterosis remains unclear up to now. In this study, a set of 184 chromosome segment substitution lines （CSSLs） population, which derived from two inbred lines Ix9801 （the recurrent parent） and Chang 72 （the donor parent）, were used as basal material to construct two test populations with the inbred lines Zheng 58 and Xun 9058. The two test populations were evaluated in two locations over two years, and the heterotic loci for plant height and ear height were identified by comparing the performance of each test hybrid with the corresponding CK at P〈0.05 significant level using one-way ANOVA analysis and Duncan＇s multiple comparisons. There were 24 and 29 different heterotic loci （HL） identified for plant height and ear height in the two populations at two locations over two years. Three HL （hlPH4a, hlPH7c, hlPHlb） for plant height and three （hlEHld, hlEH6b, hlEHlb） for ear height were identified in the CSSLs×Zheng 58 and CSSLs×Xun 9058 populations as contributing highly to heterosis performance of plant height and ear height across four environments. Among the 29 HL identified for ear height, 12 HL （41.4%） shared the same chromosomal region associated with the HL （50.0%） identified for plant height in the same test population and environment.

Effect of Dominant Semi-Dwarf Gene on Plant Height and Its Related Traits and Sensitivity to Gibberellic Acid in Rice

Six pairs of tall and dwarf near-isogenic lines derived from a dominant semi-dwarf mutant （Y98149） were selected to study height expression and sensitivity to gibberellic acid （GA3）. The lengths of the 4-5th internode, the 3rd, 2nd, 1st internodes from the top and the panicle length in the six dwarf near isogenic lines were 97.2%, 53.3%, 65.1%, 61.9% and 94.7% of those in the six tall ones, respectively, indicating that the dominant semi-dwarfing gene significantly inhibited the internode elongation. Moreover, Y98149 （mutant type） was more sensitive to GA3 than Y98148 （wild type）, and had a lower GA3 concentration in plant, about 78% of Y98148.

Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean(Glycine max L.Merr.)

With the development of sequencing technology, insertions-deletions(InDels) have been increasingly reported to be involved in the genetic determination of agronomical traits. However, most studies have focused on the identification and application of short-InDels(1–15 bp) for genetic analysis. The objective of this study was to deeply deploy long-InDels(>15 bp) for the genetic analysis of important agronomic traits in soybean. A total of 13 573 polymorphic long-InDels were identified between parents Zhongpin 03-5373(ZP) and Zhonghuang 13(ZH), which were unevenly distributed on 20 chromosomes of soybean, varying from 321 in Chr11 to 1 246 in Chr18. Consistent with the distribution pattern of annotated genes, the average density of long-InDels in arm regions was significantly higher than that in pericentromeric regions at the P=0.01 level. A total of 2 704(19.9% of total) long-InDels were located in genic regions, including 319 large-effect long-InDels, which resulted in truncated or elongated protein sequences. A previously identified QTL(qP H16) underlying plant height was further analyzed, and it was found that 26 out of 35(74.3%) long-InDel markers located in the qPH16 region showed clear polymorphisms between parents ZP and ZH. Seven markers, including three long-InDels and four previously reported SNP markers, were used to genotype 242 recombinant inbred lines derived from ZP×ZH. As a result, the qPH16 locus was narrowed from a 960-kb region to a 477.55-kb region, containing 65 annotated genes. Therefore, these long-InDels are a complementary genetic resource of SNPs and short-InDels for plant height and can facilitate genetic studies and molecular assisted selection breeding in soybean.

QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean

Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.