Genome-wide association analysis revealed that GhD6PKL2 regulates cold tolerance at seed germination and seedling emergence in cotton

The integration of cover crops into cotton (Gossypium hirsutum, L.) production remains challenging. One potential negative impact of cover crops on cotton is allelopathy. Proper selection of cover crop species and termination timing could potentially reduce the impacts of allelopathy on cotton seedlings. Two studies were conducted to determine cotton germination and growth sensitivity to cover crop leachate, which were measured using (I) five cover crops species, including: oats (Avena sativa L.), hairy vetch (Vicia Villosa), winter pea (Lathyrus hirsutus), winter wheat (Triticum aestivum), and annual rye (Lolium multiflorum), and (II) a blend of cover crops at four termination timings, including: at planting, three weeks prior to planting, six weeks prior to planting, and a split termination, where a 25 cm band in the top of the bed was terminated six weeks prior to planting, and the remaining cover crop was terminated at planting (referred to as strip 6-wk). Samples for Experiment I were collected on May 24th and for Experiment II on March 22nd (Strip/6-wk and 6-wk), April 30th (3-wk), and May 11th (at planting) in 2018. The effect of 0 (deionized water), 25, and 50 (v/v) cover crop leachate extract on cotton seed germination was evaluated in a series of controlled environmental studies. All cover crop species’ leachates negatively impacted cotton germination and seedling growth (p < 0.05). Germination inhibition rates declined numerically by species, with winter pea ≥ hairy vetch ≥ oats ≥ annual rye ≥ winter wheat at the 50 v/v concentrations. Winter pea germination inhibition on cotton equaled 47.0% and cotton radicle length was decreased by 62.8%. Termination at planting suppressed cotton germination more than the other termination timings, with the 50 v/v treatment resulting in a germination inhibition of 60.0%. Proper selection of cover crop species and termination timing prior to planting cotton will be critical in maximizing the benefits and minimizing the risks of a cover crop.

Background: Cotton is one of the important cash crops for fiber production globally. It is highly sensitive to abiotic stresses such as temperature, drought and salinity resulting in poor seedling germination and emergence leading to a decline in cotton productivity. Seed germination can be improved through physiological techniques mainly seed priming, which is a pre-sowing treatment that enables the seed to germinate more efficiently. Therefore, to assess the effects of seed priming on growth and yield production an in vivo study was performed with two different cotton cultivars (namely, BS-13 and FH-Lalazar).Methods: A field trial was conducted at Multan that comprised six treatments including T1: non-primed seeds (control) and treated seeds such as T2: hydro-priming (water), T3 & T4: hormonal priming (two different concentrations of indole acetic acid) and T5 & T6: halo-priming (two different concentrations of KNO3). The data were collected to evaluate the rate of seed germination, growth and yield of cotton under the effect of seed priming.Results: The study revealed that halo priming treatment with KNO3 enhanced the rate of seed germination by 83% as well as seedling emergence by ~90% in both cotton cultivars. Results showed that seed priming with KNO3 (3 g L-1) had the most promising effect on growth traits up to a variant extent as compared to the control plant. Meanwhile, yield attributes such as the number of cotton bolls and boll weight per plant significantly increased by 45% as compared to non-primed plants. Similarly, priming with KNO3 treatment displayed a significantly high cotton yield by 17% (767 kg ha-1) in both cotton cultivars as compared to their respective control treatment.Conclusion: Current study concluded that seed priming is an efficient and cost-effective technique that plays a vital role in better crop establishment consequently increasing germination rate, plant growth attributes and productivity of the cotton crop.Keywords: Multan; Cotton; Seed germination; Seed priming; Yield; KNO3

Magnetized water has been a promising approach to improve crop productivity but the conditions for its effectiveness remain contradictory and inconclusive. The objective of this research was to understand the influences of different magnetized water with varying quality on seed absorption, germination, and early growth of cotton. To this end, a series of experiments involving the seed soaking process, germination test, and pot experiment were carried out to study the effects of different qualities (fresh and brackish water) of magnetized water on seed water absorption, germination, seedling growth, photosynthetic characteristics, and biomass of cotton in 2018. The results showed that the maximum relative water absorption of magnetized fresh and magnetized brackish water relatively increased by 16.76% and 19.75%, respectively, and the magnetic effect time of brackish water was longer than fresh water. The relative promotion effect of magnetized brackish water on cotton seed germination and growth potential was greater than magnetized fresh water. The cotton seeds germination rate under magnetized fresh and magnetized brackish water irrigation relatively increased by 13.14% and 41.86%, respectively, and the relative promoting effect of magnetized brackish water on the vitality indexes and the morphological indexes of cotton seedlings was greater than magnetized fresh water. Unlike non-magnetized water, the net photosynthetic rate (Pn), transpiration rate (Tr), and instantaneous water use efficiency (iWUE) of cotton irrigated with magnetized water increased significantly, while the stomatal limit value (Ls) decreased. The influences of photosynthesis and water use efficiency of cotton under magnetized brackish water were greater than magnetized fresh water. Magnetized fresh water had no significant effect on biomass proportional distribution of cotton but magnetized brackish water irrigation markedly improved the root-to-stem ratio of cotton within a 35.72% range. Therefore, the magnetization of brackish water does improve the growth characteristics of cotton seedlings, and the biological effect of magnetized brackish water is more significant than that of fresh water. It is suggested that magnetized brackish water can be used to irrigate cotton seedlings when freshwater resources are insufficient.

Saline–alkali stress severely affects plant growth and productivity. Although melatonin can promote seed germination as a growth regulator, it cannot address the weak seedling growth caused by insufficient organic nutrients in saline–alkali soil. The RAE (residue after evaporation, an industrial waste from the industrial production of vitamin C) can enhance plant salt tolerance by stimulating vitamin C (ASA) synthesis and contains abundant small molecular organic acids. We hypothesized that the combined application of melatonin and RAE might synergistically enhance cotton germination and seedling growth. The cotton seeds used in this study were “Xin Lu Zhong No. 87”; a Petri dish simulation experiment and a pot experiment were conducted in 2023. Four treatments were set: control (CK), melatonin (MT), RAE (RAE), and the combined application of MT and RAE (MR). Compared to CK, MT significantly increased the germination rate of cotton seed (194.4%), while RAE significantly enhanced the underground biomass of cotton seedlings (40.3%) and ASA content (203.8%). Compared to MT and R, the combined application of melatonin and RAE significantly increased the ASA content (54.5%, 29.6%) in roots, superoxide dismutase (SOD) activity (220.3%, 89.6%) in roots, catalase (CAT) activity (15.8%, 97.5%) in leaves on the 15th day, soil cation exchange capacity (CEC) (57.2%, 9.7%), and total fresh weight (20.8%, 33.8%). Collectively, these findings indicate that the synergistic effect under the combined use of melatonin and RAE promotes cotton seed germination and seedling growth, offering a novel technical solution for salt–alkali soil cotton cultivation along with an innovative approach for the resource utilization of RAE.

Mesocotyl length is a key trait affecting seedling emergence and establishment in dry direct-seeded rice, with longer mesocotyls promoting rapid and uniform emergence, thereby forming larger effective populations. Therefore, mining genes associated with mesocotyl length will facilitate the development of rice varieties suitable for dry direct seeding. In this study, 300 rice germplasm resources with a wide range of sources were selected as experimental materials. Phenotypic traits such as mesocotyl length and seedling emergence rate were systematically determined in each variety by setting different mulch depth treatments. Genome-wide association analysis (GWAS) was used to locate QTL controlling mesocotyl length and predict candidate genes. The results showed that mesocotyl length increased significantly with greater soil cover depth, while excessively deep sowing treatments inhibited seedling emergence. The GWAS analysis identified four QTLs associated with mesocotyl length and two QTLs associated with seedling emergence, with phenotypic contributions of 6.96-8.48%. Among them, the mesocotyl length-related QTL qML3 located at 28.03-28.43 Mb on chromosome 3 was detected at both sowing depths. Gene annotation analysis identified nine candidate genes related to plant hormones and transcription factors for qML3. Further investigation revealed three genes (LOC_Os03g49250, LOC_Os03g49400, and LOC_Os03g49510) exhibiting distinct haplotypes with significant differences in mesocotyl length, suggesting they may be causal genes for qML3. The results provide new clues to elucidate the molecular mechanism of rice mesocotyl development and lay an important foundation for subsequent gene function verification and molecular breeding. In the future, the functions of these candidate genes will be verified by transgenic and other methods, and molecular markers will be developed for genetic improvement of drought-tolerant rice varieties.

Among cotton (Gossypium hirsutum L.) seeds with densities less than 1.00 g cm−3, germination performance has been shown to be proportional to the seed density. Since cotton seeds produced in the mid‐South usually attain densities higher than 1.00 g cm−3, we evaluated the germination performance of seeds with densities ranging from ≤ 1.00 to 1.10 g cm−3 to determine if the proportionality between seed density and germination performance might extend beyond 1.00 g cm−3. In laboratory, greenhouse, and growth chamber studies, maximum germination and sustained seedling growth were produced by seeds with initial densities of 1.04 and 1.06 g cm−3. The quantity of oll in the seeds was increased with seed density, but both seed weight and seed volume were decreased in the higher density seed classes. The ratio between seed oil and seed protein contents increased through a seed density of 1.06 g cm−3, then decreased slightly. Germination and seedling growth exhibited the same response to density classification as did the oil:proteln ratio. The principal deficiency of the high density cotton seeds appeared to be the low weights of cotyledonary reserves available for mobilization during germination. Selection of cotton seeds on the basis of density should therefore be done so that the small volume, light weight, but high density seeds are eliminated with the low density seeds.

Cotton (Gossypium hirsutum) is the largest fibre crop globally and an important oilseed crop. Rising temperatures and declining water supplies, which are also impacting soil salinity, threaten cotton plant productivity. Germination, emergence and young seedling stages in cotton are highly sensitive to salinity and heat stresses. Brassinosteroids (BRs) are plant steroid hormones that are essential for proper plant growth and development and also promote tolerance to a range of environmental stresses. Cotton seeds were primed with BR (24-epibrassinolide) alone or in combination with other hormones (abscisic acid, auxin and gibberellic acid) and tested for germination and early seedling growth. BR promoted germination under no stress as well as under salinity and heat stress conditions, while other hormones were ineffective under stress conditions. BR also promoted cotyledon opening and the development of lateral roots in germinated seedlings. The ability of BR to positively impact seedling growth across different stress conditions suggests that priming cotton seeds with BR may help in early and successful establishment of seedlings, which may benefit the plant through its lifecycle.

Carbon-based nanomaterials (CBNs) have great potential as a powerful tool to improve plant productivity. Here, we investigated the biological effects of graphene and carbon nanotubes (CNTs) on fiber-producing species (cotton, Gossypium hirsutum) and ornamental species (vinca, Catharanthus roseus). The exposure of seeds to CNTs or graphene led to the activation of early seed germination in Catharanthus and overall higher germination in cotton and Catharanthus seeds. The application of CBNs resulted in higher root and shoot growth of young seedlings of both tested species. Cultivation of Catharanthus plants in soil supplemented with CBNs resulted in the stimulation of plant reproductive system by inducing early flower development along with higher flower production. Catharanthus plants cultivated in CNTs or graphene supplemented soil accelerated total flower production by 37 and 58%, respectively. Additionally, CBNs reduced the toxic effects caused by NaCl. Long-term application of CBNs to crops cultivated under salt stress conditions improved the desired phenotypical traits of Catharanthus (higher flower number and leaf number) and cotton (increased fiber biomass) compared to untreated plants of both species cultivated at the same stress condition. The drought stress experiments revealed that introduction of CBNs to matured Catharanthus plant increased the plant survival with no symptoms of leaf wilting as compared to untreated Catharanthus growing in water deficit conditions.

BackgroundMeat quality related phenotypes are difficult and expensive to measure and predict but are ideal candidates for genomic selection if genetic markers that account for a worthwhile proportion of the phenotypic variation can be identified. The objectives of this study were: 1) to perform genome wide association analyses for Warner-Bratzler Shear Force (WBSF), marbling, cooking loss, tenderness, juiciness, connective tissue and flavor; 2) to determine enriched pathways present in each genome wide association analysis; and 3) to identify potential candidate genes with multiple quantitative trait loci (QTL) associated with meat quality.ResultsThe WBSF, marbling and cooking loss traits were measured in longissimus dorsi muscle from 672 steers. Out of these, 495 animals were used to measure tenderness, juiciness, connective tissue and flavor by a sensory panel. All animals were genotyped for 221,077 markers and included in a genome wide association analysis. A total number of 68 genomic regions covering 52 genes were identified using the whole genome association approach; 48% of these genes encode transmembrane proteins or membrane associated molecules. Two enrichment analysis were performed: a tissue restricted gene enrichment applying a correlation analysis between raw associated single nucleotide polymorphisms (SNPs) by trait, and a functional classification analysis performed using the DAVID Bioinformatic Resources 6.8 server. The tissue restricted gene enrichment approach identified eleven pathways including “Endoplasmic reticulum membrane” that influenced multiple traits simultaneously. The DAVID functional classification analysis uncovered eleven clusters related to transmembrane or structural proteins. A gene network was constructed where the number of raw associated uncorrelated SNPs for each gene across all traits was used as a weight. A multiple SNP association analysis was performed for the top five most connected genes in the gene-trait network. The gene network identified the EVC2, ANXA10 and PKHD1 genes as potentially harboring multiple QTLs. Polymorphisms identified in structural proteins can modulate two different processes with direct effect on meat quality: in vivo myocyte cytoskeletal organization and postmortem proteolysis.ConclusionThe main result from the present analysis is the uncovering of several candidate genes associated with meat quality that have structural function in the skeletal muscle.

Inadequate and less vigorous crop stand is a constraint to adoption of conservation tillage in cotton (Gossypium hirsutum L.) production. We evaluated the effects of tillage (conventional till, mulch‐till, no‐till), cropping system (cotton–winter fallow, cotton–winter rye, Secale cereale L.), and N source and rate (ammonium nitrate and poultry litter; 0, 100, and 200 kg N ha−1) on cotton seedling emergence on a Decatur silt loam soil (Typic Paleudults) in northern Alabama, from 1996 to 1998. Cotton seedling counts under no‐till were 40 to 150% greater than those under conventional till at 1 and 2 d during seedling emergence. Cotton–winter rye cropping system had 14 to 50% greater seedling counts than cotton–winter fallow cropping during the first 4 d of emergence in 1998. Poultry litter source of N gave 17 to 50% greater cotton seedling counts than ammonium nitrate during the first 4 d of emergence in 1998. In all these cases, the differences progressively narrowed down by the 4th day of seedling emergence. Cotton seedling counts were significantly correlated to cotton growth parameters and lint yield, especially in the drier year (1998). These results were attributed to soil moisture conservation during seedling emergence. Our results show that conservation tillage improved cotton germination, emergence, dry matter, and lint yield. Therefore, no‐till with winter rye cover cropping and poultry litter can be used for achieving early cotton seedling emergence and growth in the U.S. cotton belt where dryland cotton production systems are on the increase and safe disposal of poultry litter is becoming an environmental problem.

Eight Aspergillus spp. viz., A. flavus. A. niger. A. terreus, A. fumigatus, striatus, A. nidulans, A. tamarii and A. japonicus were isolated from the soil and the effect of spore suspensions and culture filtrates on seed germination and seedling growt of paddy, groundnut and cotton were studied. The germination of paddy seeds treate with A. flavus, A. terreus, A. nidulans and A. tamarii was 15 to 38 per cent lower thai the control. However, spore suspensions and culture filtrates of A. niger, A. terreus, A striatus and A. japonicus did not markedly affect the seed germination of groundnut an cotton and also caused post-emergence rotting. Interestingly, the seedling growth wa stimulated to different degrees by the spore supspensions as well as the culture filtrate of the eight species of Aspergilli in one or more of the three crop species studied.

Cold temperature is an important abiotic stress affecting sorghum production in temperate regions. It reduces seed germination, seedling emergence and seedling vigor thus limiting the production of the crop both temporally and spatially. The objectives of this study were (1) to assess early season cold temperature stress response of sorghum germplasm from cooler environments and identify sources of tolerance for use in breeding programs, (2) to determine population structure and marker-trait association among these germplasms for eventual development of marker tools for improving cold tolerance. A total of 136 sorghum accessions from cooler regions of the world were phenotyped for seedling growth characteristics under cold temperature imposed through early planting. The accessions were genotyped using 67 simple sequence repeats markers spanning all ten linkage groups of sorghum, of which 50 highly polymorphic markers were used in the analysis. Genetic diversity and population structure analyses sorted the population into four subpopulations. Several accessions distributed in all subpopulations showed either better or comparable level of tolerance to the standard cold tolerance source, Shan qui red. Association analysis between the markers and seedling traits identified markers Xtxp34, Xtxp88, and Xtxp319 as associated with seedling emergence, Xtxp211 and Xtxp304 with seedling dry weight, and Xtxp20 with seedling height. The markers were detected on chromosomes previously found to harbor QTLs associated with cold tolerance in sorghum. Once validated these may serve as genomic tools in marker-assisted breeding or for screening larger pool of genotypes to identify additional sources of cold tolerance.

The K+ transporter/high-affinity K+/K+ uptake (KT/HAK/KUP) family, as one of the largest K+ transporter families in higher plants, plays an essential role in plant growth, mineral element absorption, salt stress tolerance, and other physiological processes. However, little is known about this family in pear (Pyrus). Here, we identified 20 K+ transporter genes in pear (P. bretschneideri) using genome-wide analysis. Their gene structure, chromosomal distribution, conserved motifs, phylogenetics, duplication events, and expression patterns were also examined. The results of phylogenetic analysis showed that PbrKT/HAK/KUP genes were clustered into three major groups (Groups I-III). Among the 20 PbrKT/HAK/KUP genes, 18 were mapped to nine chromosomes and two to scaffolds. Four WGD/segmental gene pairs were identified, indicating that WGD/segmental duplication may have contributed to the expansion of the KT/HAK/KUP family in pear. Among the four pairs of WGD/segmentally duplicated genes, both members of three pairs had been subjected to purifying selection, whereas the fourth pair had been subjected to positive selection. Furthermore, phenotypic experiments showed that the growth of pear seedlings was affected by potassium deficiency treatment. Expression patterns of 20 PbrKT/HAK/KUP genes in roots were further assayed with qRT-PCR. PbrHAK1 and PbrHAK12/16 were significantly expressed in response to K+ deficiency, suggesting that these genes are crucial for K+ uptake in pear, especially under the condition of K+ starvation. Our results provide a foundation for further study on the function of KT/HAK/KUP genes in pear.

Grain mold is one of the most devasting diseases in sorghum [Sorghum bicolor L. (Moench)] that affects the endosperm and deteriorates the pericarp tissue, reducing the quality of the grain. Today, sorghum breeding programs have a limited number of sources of resistance for the development of resistant cultivars. Therefore, the USDA-Agriculture Research Service, National Plant Germplasm System Sudan core collection was assessed to identify new sources of grain mold resistance based on seed emergence and deterioration. A total of 246 accessions were evaluated for two years and a subset of 46 accessions with grain mold resistance were subsequently evaluated for two additional years together with 11 breeding resistant lines from the sorghum association panel. The analysis identified 39 grain mold resistance accessions including seven that showed both high seedling emergence (> 82%) and low seed deterioration (< 2.15). Phylogenetic analysis revealed that five accessions (PI 570382, PI 570776, PI 570330, PI 570702, and PI 570348) that clustered distantly from reference sets and showed both high seedling emergence and low seed deterioration can be classified as new resistance sources. Genome-wide association analysis using 147,069 SNPs identified two genomic regions in chromosome 2 and 3 associated with seedling emergence rate and seed deterioration, respectively. The analysis of both genomic regions found two genes of interest associated with phenylpropanoid metabolic process and phosphorylase kinase. These Sudanese grain mold resistance accessions provide new genetically diverse germplasm for breeding programs and insights in the defense resistance responses.

Neutralizing acid residues on cottonseed after HCl delinting contributed to seedling emergence and survival in field plantings and emergence in greenhouse plantings, but not necessarily to survival in the greenhouse where seedling diseases were severe or to germination in the laboratory. Similar results were obtained with an experimental neutralizer (EN) and the standard neutralizer (NH3) used alone or in combination with fungicides and the insecticide, disulfoton. The percentage of plants with foliar symptoms of Verticillium wilt was reduced by the neutralizers and pesticides. Decrease in wilt symptoms was related to increased plant populations. Percentage germination, emergence and survival of seedlings and Verticillium wilt were similar when EN and pesticides were applied simultaneously or sequentially. Use of EN can eliminate ammonia and ammonium chloride pollutants currently associated with acid delinting of cottonseed.