Plants lack behavioral responses to avoid dramatic environmental changes associated with the annual seasons. For survival, they have evolved complex sensory systems to sense fluctuations in light and optimize their architecture in response to changes in these cues. Phytochrome A (phyA) was initially identified as a photoreceptor that senses far-red light signals. It was then identified as playing a central role in promoting hypocotyl growth, fiber development, and flowering time in a variety of plants including Arabidopsis, rice, soybean and cotton. Under dark conditions, phyA is present in the cytoplasm in the physiologically inactive (Pr) form. Far-red light signals induce the transformation of Pr into the physiologically active (Pfr) form, after which Pfr-phyA is recognized by FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL) and translocated to the nucleus, initiating a series of signaling cascades. The current review comprehensively summarizes recent advances in understanding the function of phyA in plants, including phyA-mediated shade avoidance and flowering time. Remaining issues and possible directions for future research on phyA are also discussed.

The boll opening rate (BOR) is an early maturity trait that plays a crucial role in cotton production in China, as BOR has a significant effect on defoliant spraying and picking time of unginned cotton, ultimately determining yield and fiber quality. Therefore, elucidating the genetic basis of BOR and identifying stably associated loci, elite alleles, and potential candidate genes can effectively accelerate the molecular breeding process. In this study, we utilized the mixed linear model (MLM) algorithm to perform a genome-wide association study (GWAS) based on 4,452,629 single-nucleotide polymorphisms (SNPs) obtained through whole-genome resequencing of a natural population of 418 upland cotton accessions and phenotypic BOR data acquired from five environments. A total of 18 SNP loci were identified on chromosome D11 that are stable and significantly associated with BOR in multiple environments. Moreover, a significant SNP peak (23.703–23.826 Mb) was identified, and a GH-D11G2034 gene and favorable allelic variation (GG) related to BOR were found in this genomic region, significantly increasing cotton BOR. Evolutionary studies have shown that GH-D11G2034 may have been subjected to artificial selection throughout the variety selection process. This study provides valuable insights and suggests that the GH-D11G2034 gene and its favorable allelic variation (GG) could be potential targets for molecular breeding to improve BOR in upland cotton. However, further research is needed to validate the function of this gene and explore its potential applications in cotton breeding programs. Overall, this study contributes to the advancement of genetic improvement in early maturity and has important implications for the sustainable development of the cotton industry.

Background: Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) technology has advanced rapidly; however, current protoplast-based methods for evaluating genome-editing efficiency rely on expensive instruments and are incompatible with certain experimental strategies, highlighting the urgent need for a simple, cost-effective alternative. Results: In this study, we developed a visual system for assessing genome-editing efficiency in cotton using GhF3H , a key gene involved in anthocyanin biosynthesis whose knockout results in distinct changes in tissue coloration. The red-background cotton line RZM24 was obtained via hybridization and backcrossing. Expression vectors harboring Cas9, Cas12a, or CasΦ and their corresponding single-guide RNAs (sgRNAs) targeting GhF3H were constructed and introduced into hypocotyls via Agrobacterium -mediated transformation, followed by callus induction. Successfully edited calli exhibited white or white-and-red chimeric phenotypes, whereas unedited calli remained red. Cas9 showed the highest editing efficiency, followed by Cas12a, with CasΦ showing the lowest. Genotyping confirmed that white and chimeric calli were capable of regenerating plants carrying heritable mutations, and the three Cas systems induced distinct mutation types. Conclusions: This system enables rapid visual screening of editing events within 45 days, facilitating the comparison of CRISPR toolkits, validation of novel nucleases, and optimization of sgRNA delivery strategies. This approach may be adaptable to other crops and offers a practical solution to advance plant genome engineering.

Upland cotton (Gossypium hirsutum L.) dominates Xinjiang’s cotton production, but the narrow genetic base of modern cultivars limits further yield gains. Here, 356 Xinjiang upland cotton accessions (184 northern, 172 southern) were genotyped at 280 elite trait locus–trait combinations (270 unique markers) using a liquid-phase chip. Pairwise kinship was inferred with the KING-robust estimator and cross-validated by IBS similarity, population structure was examined by PCA, and a marker-weighted comprehensive elite genotype index (S) was constructed. The overall missing rate was 0.43%, and five identical and 101 near-identical accession pairs were detected. PC1 and PC2 explained only 9.81% and 7.29% of the variation, with substantial regional overlap. Index S ranged from 0.39 to 0.57, led by Tkuo, Y80, Ba 44435, Ziyu R040068 and Youzhi 5; salt tolerance (0.07), lint yield (0.14), seed index (0.19) and fiber strength (0.22) showed the lowest carriage of the marker-defined elite alleles scored here. After excluding close relatives, 62,252 crosses (98.52%) satisfied the constraint, and 30 crosses (19 inter-regional) were recommended, the best being Ziyu TY112 × Tkuo (joint coverage U = 0.65). These parents and crosses provide candidates for parental selection, pending field validation.

Upland cotton (Gossypium hirsutum L.) dominates Xinjiang's cotton production, but the narrow genetic base of modern cultivars limits further yield gains. Here, 356 Xinjiang upland cotton accessions (184 northern, 172 southern) were genotyped at 280 elite trait locus–trait combinations (270 unique markers) using a liquid-phase chip. Pairwise kinship was inferred with the KING-robust estimator and cross-validated by IBS similarity, population structure was examined by PCA, and a marker-weighted comprehensive elite genotype index (S) was constructed. The overall missing rate was 0.43%, and five identical and 101 near-identical accession pairs were detected. PC1 and PC2 explained only 9.81% and 7.29% of the variation, with substantial regional overlap. Index S ranged from 0.39 to 0.57, led by Tkuo, Y80, Ba 44435, Ziyu R040068 and Youzhi 5; salt tolerance (0.07), lint yield (0.14), seed index (0.19) and fiber strength (0.22) were the main deficiencies. After excluding close relatives, 62,252 crosses (98.52%) satisfied the constraint, and 30 crosses (19 inter-regional) were recommended, the best being Ziyu TY112 × Tkuo (joint coverage U = 0.65). These parents and crosses provide candidates for parental selection, pending field validation.