## 4 Discussion
There are consensus or physical close loci among previous studies and this study, such as the interval of SNPs of A01_1783865 for PH, A03_6291348 for BN, A07_10401876, and A07_11506350 for TSW. These results demonstrate the reliability of this report and provide potential loci for controlling agronomic traits. Some pleiotropic SNPs were also detected, including A01_1783685 (PH and SYP), C06_26638717 (PH and NSS), and C03_4731660 (MIL and MINS), which might be the loci playing multiple roles during plant development. Besides, 12 promising novel significant SNPs were detected that are related to BN (A05_19368584 and A05_19764389), SL (A06_23598999, A06_23608274, and C07_38735522), PH (C04_47349279, C04_47585236, and C09_36899680), MINS (C05_6251826), NSS (C06_22559430 and C06_22570315), and HI (C05_6554451). HI is mainly related to plant height, infloresances, flower, pod, branches, and flowers, which is also influenced by environmental conditions such as light, temperature, and nutrient status [45]. Gene functions and expressions help predict candidate genes controlling the traits. In this study, 39 candidate genes were predicted in 22 significant SNP intervals, all of which were highly expressed in relative tissues and involved in the development of cell wall, flower, xylem, and whole plant. The important candidate genes were discussed as follows. Within the interval of C05_6554451 for HI, _BnaC05g11350D_ codes the CRP protein, while CRPs function as regulators of cell-cell communication in plants, and participate in plant growth, pollen tube growth, and fertilization process [46; 47; 48]. Plant development is the process of cell division, growth and differentiation. Among these genes, _CDC20_, identified by A01_1783685 and A01_1565817 for PH and SYP, encodes a cell division cycle 20 protein that is indispensable for normal plant development and fertility. In this region, _SLOMO_ coding an F-box protein is considered as a candidate gene. In _Arabidopsis thaliana_, the rate of inflorescence meristems organ formation of the _slamo_ mutant is significantly reduced, indicating SLOMO regulates organ initiation at the shoot meristem [49]. _KTNA1_ was detected on A07_random for NSS, whose orthologs in _Arabidopsis thaliana_ were shown to control cell plate/daughter wall formation [50]. _HRGP_ located on C05 was identified for MINS, encoding a hydroxyproline-rich glycoprotein family protein that functions in early leaf and root vascular differentiation [51]. Floral organogenesis plays a vital role in plant height, branch number, branch angel, main inflorescence length, silique length and width, and number of seeds per silique. In this study, five genes, _AG1_, _BNQ2_, _TRANS11_, _EBS_, _FTM4.1_, and _FTM4.2_, were predicted as the requirements for floral organ growth in _Arabidopsis thaliana_[52; 53; 54; 55; 56]. For example, _AG1_ is a floral homeotic gene encoding a MADS domain transcription factor, suppression of which favors a reversion of floral meristems from determinate to indeterminate development [52]. _FTM4_, encoding a leucine-rich repeat protein, is induced in the early inflorescence meristem, and mutations of _FTM4_ delay flowering [53]. The phenotypes of _bmq2_ and _bmq3_ mutants show pale-green sepals and carpels, and purple inflorescents stems and siliques [54], and the double or high order mutants show dwarf vegetative growth and reduced fertility with unequal genetic redundancy [55]. Moreover, we identified some genes functioningin pollen germination and tube growth, including _PGF10_ and _RPL32A_. All of these genes showed high expressions in the inflorescence tips, silique pericarp, and stems (Figure 6). Three candidate genes were related to fiber and pectin involved in SL, PH, and NSS. _UBQ5_ and _QULA2_, encoding pectin methyl esterase and pectin methyltransferase, respectively, participate in cell wall formation [57; 58; 59]. _qua2_ showed a 50% reduction in homogalacturonan content compared with the wild type [59].