Sorghum is mainly used as a human food and beverage source, playing an important role in the production of ethanol and other bio-industrial products. Thus it is regarded as a model crop for energy plants. Genetic map construction is the foundation for marker-assisted selection and gene cloning. So far several sorghum linkage maps have been reported using different kinds of molecular markers. However marker numbers and chromosome coverage are limited. As a result, it is difficult to get consistent results and the maps are hard to unify. In the present study, the genomes of 130 individuals consisting an F2 population together with their parents were surveyed using a high-throughput sequencing technique. A high-density linkage map was constructed using specific-locus amplified fragments (SLAF) markers. This map can provide information and serve as a reference for effective gene exploration, and for marker assisted-breeding program. A high-throughput sequencing method was adopted to screen SLAF markers with 130 F2 individuals from a cross between a grain sorghum variety, J204, and a sweet sorghum variety, Keter. In the present study, 52,928 suitable SLAF markers out of 43,528,021 pair-end reads were chosen to conduct genetic map construction, 12.0% of which were polymorphic. Among the 6353 polymorphic SLAF markers, 5829 (91.8%) were successfully genotyped in the F2 mapping population. Finally 2246 SLAF markers were obtained to construct a high-density genetic linkage map. The total distance of linkage map covering all 10 chromosomes was 2158.1 cM. The largest gap on each chromosome was 10.2 cM on average. The proportion of gaps less than and/or equal to 5.0 cM was averagely 98.1%. The markers on each chromosome ranged from 123 (chromosome 9) to 315 (chromosome 4) with a mean value of 224.6, the distance between adjacent markers ranged from 0.6 (chromosome 10) to 1.3 cM (chromosome 9) with an average distance of only 0.98 cM. A high density sorghum genetic map was constructed in this study. The total length was 2158.1 cM covering all 10 chromosomes with a total number of 2246 SLAF markers. The construction of this map can provide detailed information for accurate gene localization and cloning and application of marker-assisted breeding.

Amino acid/auxin permease (AAAP) genes encode a large family of protein transporters that play important roles in various aspects of plant growth and development. Here, we performed genome-wide identification of members in the foxtail millet (Setaria italica L.) AAAP family (SiAAAP) and their saline-alkali stress-induced expression patterns, resulting in the identification of 65 SiAAAP genes, which could be divided into eight subfamilies. Except for SiAAAP65, the remaining 64 genes were located on nine chromosomes of foxtail millet. Gene structure and conserved motif analyses indicated that the members in the same subfamily are highly conserved. Gene duplication event analysis suggested that tandem duplication may be the main factor driving the expansion of this gene family, and Ka/Ks analysis indicated that all the duplicated genes have undergone purifying selection. Transcriptome analysis showed differential expression of SiAAAPs in roots, stems, leaves, and tassel inflorescence. Analysis of cis-acting elements in the promoter indicated that SiAAAPs contain stress-responsive cis-acting elements. Under saline-alkali stress, qRT-PCR analysis showed that SiAAP3, SiLHT2, and SiAAP16 were differentially expressed between salt-alkali tolerant millet variety JK3 and salt-alkali sensitive millet variety B175. These results suggest that these genes may be involved in or regulate the response to saline-alkali stress, providing a theoretical basis for further studying the function of SiAAAPs.

E3 ubiquitin ligases are central modifiers of plant signaling pathways that regulate protein function, localization, degradation, and other biological processes by linking ubiquitin to target proteins. E3 ubiquitin ligases include proteins with the U-box domain. However, there has been no report about the foxtail millet (Setaria italica L. Beauv) U-box gene family (SiPUB) to date. To explore the function of SiPUBs, this study performed genome-wide identification of SiPUBs and expression analysis of them in response to saline-alkali stress. A total of 70 SiPUBs were identified, which were unevenly distributed on eight chromosomes. Phylogenetic and conserved motif analysis demonstrated that SiPUBs could be clustered into six subfamilies (I–VI), and most SiPUBs were closely related to the homologues in rice. Twenty-eight types of cis-acting elements were identified in SiPUBs, most of which contained many light-responsive elements and plant hormone-responsive elements. Foxtail millet had 19, 78, 85, 18, and 89 collinear U-box gene pairs with Arabidopsis, rice, sorghum, tomato, and maize, respectively. Tissue specific expression analysis revealed great variations in SiPUB expression among different tissues, and most SiPUBs were relatively highly expressed in roots, indicating that SiPUBs may play important roles in root development or other growth and development processes of foxtail millet. Furthermore, the responses of 15 SiPUBs to saline-alkali stress were detected by qRT-PCR. The results showed that saline-alkali stress led to significantly differential expression of these 15 SiPUBs, and SiPUB20/48/70 may play important roles in the response mechanism against saline-alkali stress. Overall, this study provides important information for further exploration of the biological function of U-box genes.

The utilization of crop heterosis can greatly improve crop yield. The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.). The chloroplast genomes of two sterile lines and one maintainer were sequenced using second-generation high-throughput technology and assembled. The nonsynonymous mutated genes among the three varieties were identified, the expressed difference was further analyzed by qPCR, and finally, the function of the differentially expressed genes was analyzed by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method. A total of 16 genes containing 31 nonsynonymous mutations between K519A and 519B were identified. There were no base mutations in the protein-encoding genes between K519A and YS3038. The chloroplast genomes of 519B and K519A were closely related to the Triticum genus and Aegilops genus, respectively. The gene expression levels of the six selected genes with nonsynonymous mutation sites for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development. The seed setting rates of atpB-silenced or ndhH-silenced 519B plants by BSMV-VIGS method were significantly reduced. It can be concluded that atpB and the ndhH are likely to be involved in the reproductive transformation of 519B.

Dehydration response element binding proteins (DREBs) play a vital role in transcriptional regulators in enhancing plant tolerance to abiotic stress. To investigate the biological functions of the DREB gene family (SiDREBs) in foxtail millet (Setaria italica), this study performed bioinformatics and gene expression analysis on SiDREBs under abiotic stress. A total of 166 family members of SiDREBs were identified, which were classified into six subfamilies. SiDREBs were unevenly distributed on nine chromosomes, and were designated as SiDREB1–166 based on their chromosomal positions. Covariance analysis revealed that SiDREBs were much more closely related to monocotyledonous plants sorghum, maize, and rice than to dicotyledonous plants Arabidopsis thaliana, tomato, and soybean. Promoter cis-acting element analysis showed that SiDREBs contained stress-related cis-acting elements. Under saline-alkali stress, SiDREB153 exhibited significantly different expression levels between the resistant and susceptible materials, indicating that it plays a positive regulatory role in the response of foxtail millet to saline-alkali stress. Among different abiotic stresses, the expression of SiDREB80 increased under drought, saline-alkali, and shade stress, that of SiDREB4/129/131 rose under saline-alkali and high temperature stress, and that of SiDREB159 increased under herbicide and saline-alkali stress. These genes play an important role in the response of foxtail millet to stress. These findings provide a theoretical basis for further studies on the function of SiDREBs in response to abiotic stress.

Unreasonable fertilization practices are still applied in agricultural production, resulting in reduced crop yields and wasting resources. Therefore, it is essential to optimize fertilization regimes to improve the nutrient absorption capacity of crops. However, the effects of combining nitrogen, phosphorus, and potassium (NPK) compound fertilizer with biochar on the uptake and utilization of phosphorus (P) by wheat and soil fertility remain poorly understood. Thus, we tested three biochar levels (0 quintal (q) ha ⁻¹ (B1), 75 q ha ⁻¹ (B2), and 150 q ha ⁻¹ (B3)) and four compound fertilizer levels (0 q ha ⁻¹ (F1), 2.25 q ha ^–1 (F2), 4.50 q ha ⁻¹ (F3), and 6.75 q ha ⁻¹ (F4)), and compared the effects of different experimental combinations across two years. The results showed that combined application could increase the wheat yield, soil P content, accumulated plant P, and P utilization efficiency. Among the different treatments, the wheat yields in both years were highest under B2F3, and the total soil P contents in the booting and flowering stages were also the highest. The soil available P contents in the jointing stage, booting stage, and flowering stage were highest under B3F3. The available P soil contents at maturity in both years were highest under B3F4. In addition, compared with B1F4, the accumulated plant P amounts in the booting and flowering stages were 17.6–77.3% and 17.0–87.3% higher, respectively, under B2F2, B2F3, B3F2, and B3F4 ( P < 0.05). The accumulated plant P amounts in the maturity stage during the two years were highest under B2F3 (0.83 q ha ⁻¹ ) and B3F3 (0.42 q ha ⁻¹ ), respectively. Moreover, the partial factor productivity and agronomic use efficiency were significantly higher under B2F2, B2F3, B3F2, and B3F3 than B1F4. In summary, under the experimental conditions in this study, applying compound fertilizer at 4.50 q ha ⁻¹ combined with biochar at 75 q ha ⁻¹ is recommended as the optimal fertilization scheme.