Cotton fiber is the most important natural raw material for the textile industry, and fiber length (FL) is one of the most important traits in cotton. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for FL. In our study, two backcrossed inbred lines (BILs) were chosen as parents to construct a high-density genetic map in F₂ which was used to fine map FL QTL in F_2:3 population. The genetic map had a total size of 3462.8?cM, containing 9182 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing. Two FL related stable QTL were identified on two chromosomes (qFL-A08-1 on A08 and qFL-D03-1 on D03), and qFL-A08-1 was confirmed by a meta-analysis. Utilizing previously obtained RNA-seq data for the two BILs and qRT-PCR analysis, two candidate genes annotated as cytochrome b5 (CB5, Gh_A08G1729) and microtubule end-binding 1C (EB1C, Gh_D03G0232) that may regulate FL during the fiber elongation stage were identified. In addition, nine recombination hotspots in this population were found. The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of fiber elongation.

Pure lines derived from multiple parents provide abundant variation for genetic study. However, efficient genetic analysis methods and user-friendly software are still lacking. In this study, we developed linkage analysis methods and integrated analysis software for pure-line populations derived from four-way and eight-way crosses. First, polymorphic markers are classified into different categories according to the number of identifiable alleles in the inbred parents. Expected genotypic probability is then derived for each pair of complete markers, and based on them a maximum likelihood estimate (MLE) of recombination frequency is calculated. An EM algorithm is proposed for calculating recombination frequencies in scenarios that at least one marker is incomplete. A linkage map can thus be constructed using estimated recombination frequencies. We describe a software package called GAPL for recombination frequency estimation and linkage map construction in multi-parental pure-line populations. Both simulation studies and results from a reported four-way cross recombinant inbred line population demonstrate that the proposed method and software can build more accurate linkage maps in shorter times than other published software packages. The GAPL software is freely available from www.isbreeding.net and can also be used for QTL mapping in multi-parental populations.

Wheat powdery mildew (Blumeria graminis f. sp. tritici, Bgt) is a disease of increasing importance globally due to the adoption of high yielding varieties and modern sustainable farming technologies. Growing resistant cultivars is a preferred approach to managing this disease, and novel powdery mildew resistance genes are urgently needed for new cultivar development. A genome-wide association study was performed on a panel of 1292 wheat landraces and historical cultivars using 5011 single nucleotide polymorphism (SNP) markers. The association panel was evaluated for reactions to three Bgt inoculants, OKS(14)-B-3-1, OKS(14)-C-2-1, and Bgt15. Linkage disequilibrum (LD) analysis indicated that genome-wide LD decayed to 0.1 at 23 Mb, and population structure analysis revealed seven subgroups in the panel. Association analysis using a mixed linear model (MLM) identified three loci for powdery mildew resistance on chromosome 2B, designated QPm.stars-2BL1, QPm.stars-2BL2, and QPm.stars-2BL3. To evaluate the efficacy of GWAS in gene discovery, QPm.stars-2BL2 was validated using F₂ and F_2:3 populations derived from PI 420646?×?OK1059060-126135-3. Linkage analysis delimited the powdery mildew resistance gene in PI 420646 to an interval where QPm.stars-2BL2 was located, lending credence to the GWAS results. QPm.stars-2BL1 and QPm.stars-2BL3, which were associated with four SNPs located at 457.7-461.7?Mb and two SNPs located at 696.6-715.9?Mb in the Chinese Spring reference IWGSC RefSeq v1.0, respectively, are likely novel loci for powdery mildew resistance and can be used in wheat breeding to improve powdery mildew resistance.

Cucumber mosaic virus (CMV) is one of the most severe viral diseases transmitted by aphids infecting Solanum crops in China, causing great losses of crop yields and income in rural communities. The tobacco cultivars NC82 and Taiyan 8 are closely related but differ in resistance to CMV. NC82 is susceptible to infection and Taiyan 8 is resistant, but the mechanisms underlying this difference in resistance are not clear. In this study, we conducted RNA sequencing to analyze changes in gene expression induced in the leaves of Taiyan 8 and NC82 upon systemic infection with CMV, compared with gene expression in the leaves of mock-inoculated plants. Leaves were sampled at one, three, eight, and 15?days after infection. In total, 3443 and 747 differentially expressed genes were identified in Taiyan 8 and NC82, respectively. Gene ontology and pathway enrichment analyses revealed that the different responses to CMV infection between cultivars were based on microtubule-based processes, pentose and glucuronate interconversions, plant-pathogen interaction, and hormone signal transduction pathways. Genes encoding pathogenesis-related proteins, disease-resistance proteins, lipoxygenase, cellulose synthase, an auxin response factor, and an ethylene receptor showed different expression patterns. The differences in gene expression following CMV infection likely contributed to the different resistance levels of these two tobacco cultivars. The comprehensive transcriptome dataset described here, which includes candidate response genes, will serve as a resource for further studies of the molecular mechanisms associated with tobacco defense responses against CMV.

Worldwide, scarce water resources and substantial food demands require efficient water use and high yield. This study investigated whether irrigation frequency can be used to adjust soil moisture to increase grain yield and water use efficiency (WUE) of high-yield maize under conditions of mulching and drip irrigation. A field experiment was conducted using three irrigation intervals in 2016: 6, 9, and 12?days (labeled D6, D9, and D12) and five irrigation intervals in 2017: 3, 6, 9, 12, and 15?days (D3, D6, D9, D12, and D15). In Xinjiang, an optimal irrigation quota is 540?mm for high-yield maize. The D3, D6, D9, D12, and D15 irrigation intervals gave grain yields of 19.7, 19.1-21.0, 18.8-20.0, 18.2-19.2, and 17.2?Mg?ha⁻¹ and a WUE of 2.48, 2.53-2.80, 2.47-2.63, 2.34-2.45, and 2.08?kg?m⁻³, respectively. Treatment D6 led to the highest soil water storage, but evapotranspiration and soil-water evaporation were lower than other treatments. These results show that irrigation interval D6 can help maintain a favorable soil-moisture environment in the upper-60-cm soil layer, reduce soil-water evaporation and evapotranspiration, and produce the highest yield and WUE. In this arid region and in other regions with similar soil and climate conditions, a similar irrigation interval would thus be beneficial for adjusting soil moisture to increase maize yield and WUE under conditions of mulching and drip irrigation.

With global warming, rice plants may be subjected to heat stress more regularly during the heat-sensitive flowering stage, causing spikelet sterility and grain yield loss. Stigma exsertion is considered to increase pollen reception and promote female reproductive success. The aim of this study was to investigate the role of stigma exsertion on spikelet fertility at high temperatures. Five rice cultivars (Liangyoupeijiu, Shanyou 63, Huanghuazhan, Nagina 22, and IR64) with differing degrees of stigma exsertion were cultivated and exposed to high temperature at anthesis. Heat-tolerant cultivars did not always show a high percentage of spikelets with exserted stigmas, and vice versa. Irrespective of the presence of more pollen grains on exserted stigmas, spikelets with exserted stigmas did not show greater spikelet fertility than spikelets with fewer exserted stigmas or hidden stigmas under heat stress. GA₃ application augmented the percentage of spikelets with exserted stigmas; however, it did not increase spikelet fertility under heat stress. Spikelet fertility of whole panicles was negatively correlated with the percentage of spikelets with exserted stigmas, but positively with that with hidden stigmas. Viability of the hidden stigmas was less reduced than that of exserted stigmas under heat stress, suggesting that hidden stigmas have an advantage in maintaining viability. Heat stress delayed anther dehiscence and reduced the viabilities of both exserted stigmas and pollens, thereby causing low spikelet fertility. Together, these results suggest that high spikelet fertility does not depend on stigma exsertion and that enclosed stigma generally contributes to higher spikelet fertility and heat tolerance under high-temperature conditions during flowering in rice.

Stigma exsertion in male sterile lines of hybrid rice is important for seed yield. In the present study, ZS616 [Oryza sativa subsp. Xian (indica)], a male sterile line with a stigma exsertion rate (SER) as high as 94.5%, was crossed to DS552, a japonica line with almost no exserted stigmas. F₃ plants with extremely low and high SER were sequenced to identify SER-associated quantitative trait loci (QTL). A major QTL for SER, qSER-3.1, was identified along with other QTL on chromosome 3 in a 3.9?Mb region. A total of 307 nonsynonymous single-nucleotide polymorphisms (SNPs) and 27 frame-shift insertion/deletions (InDels) differentiating ZS616 and DS552 were identified in the region containing qSER-3.1. Most SNPs (294) and InDels (25) were excluded after further analysis because they were shared by ZS616 and low (<2.0%) SER accessions in the Huazhong Agricultural University (HAU) core rice collection. Association analysis using the full HAU collection identified a 17-bp InDel in OS03G0689400 as the most likely causal genetic variant underlying qSER-3.1. ZS616-type accessions (n?=?54, with the 17-bp insertion) in the HAU collection had minimum (16.5%) and mean (39.6%) SERs significantly greater than those (n?=?424) without the insertion (with minimum and mean SERs of 0.2% and 20.6%, respectively). Thus, this study identified a major QTL for stigma exsertion and revealed the mutation in a candidate gene for the QTL.

Staygreen syndrome or Zhengqing in soybean has recently become a major issue for Chinese growers in the Huang-Huai-Hai river basin. Although previous studies revealed that staygreen can be induced when pods/seeds are damaged, it is unknown whether virus infection or insect infestation causes staygreen. To determine whether viral infection causes staygreen, a survey of soybean staygreen incidence in the Huang-Huai-Hai river basin was conducted in 2016 and 2017. Diseased samples were collected and analyzed using DAS-ELISA for Soybean mosaic virus, Watermelon mosaic virus, Bean pod mottle virus, Cucumber mosaic virus, and Bean common mosaic virus. The survey showed that the severity of soybean staygreen syndrome was most prevalent in Beijing, Henan, Shaanxi, and some parts of Shandong provinces, with yield losses from 0 to nearly 100%, but only a small fraction of samples were positive for the tested viruses. A field cage experiment and an insecticide treatment field trial were conducted to determine the contribution of the bean bug, Riptortus pedestris, to staygreen incidence. The field cage experiment showed that R. pedestris treatment resulted in shorter plants, more empty pods, increased numbers of abnormal seeds, and decreased yields. The field experiment showed that there were fewer R. pedestris and less soybean staygreen incidence in fields treated with insecticide than in untreated control fields. Together, these results suggest that R. pedestris infestation rather than virus infection induces staygreen syndrome and that growers in this region can mitigate staygreen syndrome via bean bug control.

The development of green super rice varieties with improved nutrient use efficiency (NuUE) is a vital target area to increase yield and make it more stable under rainfed conditions. In the present study, we followed an early backcross (BC) breeding approach by using a high-yielding and widely adapted Xian variety, Weed Tolerant Rice 1 (WTR-1), as a recipient and a Geng variety, Hao-An-Nong (HAN), as a donor. Starting from the BC₁F₂ generation, the BC population went through one generation of selection under irrigated, low-input, and rainfed conditions, followed by four consecutive generations of screening and selection for high grain yield (GY) under six different nutrient conditions (NPK, 75N, -N, -P, -NP, and -NPK), leading to the development of 230 BC₁F₆ introgression lines (ILs). These 230 ILs were evaluated under the same six nutrient conditions for 13 agro-morphological and grain yield component traits in comparison to four checks and parents. Significant trait variations were observed between the treatments and ILs. Positive correlations were identified for GY with biomass, panicle length, flag-leaf area, flag-leaf width, filled grain number per panicle, 1000-grain weight, and tiller number under -N, -P, -NP, and -NPK conditions. Out of 230 ILs, 12 were identified as promising under two or more nutrient deficiency conditions. The results demonstrated an efficient inter-subspecific BC breeding procedure with a first round of selection under rainfed-drought conditions, followed by four generations of progeny testing for yield performance under six nutrient conditions. The promising ILs can be useful resources for molecular genetic dissection and understanding the physiological mechanisms of NuUE.

Xiaoyan 60 (XY60) is a new wheat variety bred in the laboratory of Zhensheng Li. After salt treatment, seedlings of XY60 maintain green leaves and produce longer roots than the high yielding cultivar Zhongmai 175 (ZM175). To explain these different phenotypes we carried out an RNA-Seq analysis using 12 samples from three tissues of both varieties subjected to salt and control treatments. By comparing data from the salt treated plants with the control, 703, 979, and 1197 differentially expressed genes (DEGs) were detected in new leaves, old leaves, and roots of XY60, respectively. The corresponding numbers for ZM175 were 613, 1401, and 1301. The most significantly enriched Gene Ontology (GO) terms and KEGG pathways were associated with polyunsaturated fatty acid (PUFA) metabolism in both new and old leaves from XY60. They were associated with photosynthesis and energy metabolism in ZM175. The most significantly enriched KEGG pathway in roots of both varieties was “glucosinolate biosynthesis”. In addition, jasmonic acid (JA) concentration in XY60 was higher than in ZM175, although it increased significantly in both varieties following salt treatment. Trends in relative expression levels of AOS, MYC2, and JAZ revealed by qRT-PCR were concordant with those from RNA-Seq. Our results suggest that PUFAs may contribute to salt tolerance in common wheat by enhancing the photosynthetic system and JA-related pathways.

WRKY transcription factors (TFs) play important roles in the regulation of biotic and abiotic stresses. However, the functions of most WRKY TFs in upland cotton (Gossypium hirsutum) are still unknown. In this study, we functionally identified a group III WRKY transcription factor, GhWRKY70, in upland cotton. Reverse transcription-quantitative PCR analysis showed that GhWRKY70 expression was induced by Verticillium dahliae, salicylic acid (SA) and methyl jasmonate. Virus-induced gene silencing of GhWRKY70 increased the resistance of cotton to V. dahliae. Specifically, jasmonic acid (JA) response-associated genes were upregulated and SA-related genes were downregulated in GhWRKY70-silenced cotton plants. Overexpression of GhWRKY70 reduced tolerance to V. dahliae in Arabidopsis thaliana. Transgenic Arabidopsis plants showed increased expression of SA-associated genes and reduced expression of JA response-associated genes. These results suggest that GhWRKY70 negatively regulates tolerance to V. dahliae in at least two ways: (i) by upregulating the expression of SA-associated genes and (ii) by reducing the expression of JA-associated genes.

Late embryogenesis abundant (LEA) proteins accumulate in the late stage of plant seed development, and are upregulated in most plants during drought, cold, heat, or salinity stress. LEA proteins can be classified by amino-acid sequence into seven groups. Dehydrins belong to LEA protein group II. In previous studies, the maize KS type dehydrin ZmDHN13 increased the tolerance of transgenic tobacco to oxidative stress. In the present study, ZmDHN13 was identified under copper stress conditions, and the protein was then characterized using transgenic yeast and tobacco plants to investigate its functions. ZmDHN13 bound Cu²⁺. Its overexpression in transgenic tobacco conferred tolerance to copper stress by binding metals and reducing the accumulation of reactive oxygen species (ROS). Three conserved domains displayed a cooperative effect under copper stress conditions.

Brassinosteroids (BRs) are endogenous phytohormones that play important roles in regulating plant growth and development. In this study, we evaluated the effects of brassinolide (BL, one of the active BRs) on soybean and identified roles of the hormone in regulating multiple aspects of plant growth and development. BL application promoted hypocotyl and epicotyl elongation in the light but blocked epicotyl elongation in the dark. High levels of castasterone and BL accumulated in light-grown plants. BL disrupted shoot negative gravitropism, whereas gibberellin did not. BL delayed leaf senescence. Transcriptome analysis showed that BL induced cell wall-modifying genes and auxin-associated genes but suppressed a class of WRKY genes involved in senescence and stress responses, showing the complex roles of BRs in multiple biological processes.