Global agriculture is facing severe challenges, and breeding technology is the foundation and key to the development of the seed industry. Gene editing technology refers to the precise modification of target genes to achieve deletion, insertion, and replacement of specific target gene fragments. It can precisely modify target genes or introduce certain excellent genes into crops to produce crops with excellent agronomic traits, which has great potential in molecular design breeding and is of great significance to ensuring food security. Weed damage has a huge impact on the yield and quality of crops. To control weed damage efficiently, safely and sustainably has always been a hot research topic. Currently, more than 200 types of chemical herbicides have emerged in the global market. Using chemical methods to control weeds has become an important part of modern agriculture, and the cost of weed control has been significantly reduced by promoting herbicide-resistant crops. However, with the large-scale promotion of herbicide-resistant crops and the long-term use of single herbicides, environmental safety problems such as weed resistance and escape of resistant genes have gradually been discovered. Currently, the development of functional genomics, bioinformatics and genetic engineering technology (especially the widespread application of gene editing technology in plants) has created conditions for the creation of herbicide-resistant crops and new efficient weed control systems. In this article, the main target genes of herbicides that inhibit amino acid biosynthesis, lipid metabolism, carotenoid, plastoquinone and tocopherol biosynthesis pathways and their action mechanisms are introduced at first. Secondly, two methods for mining new herbicide resistance genes and herbicide systems are introduced, including the directed mutation method of herbicide resistance genes within crops based on CRISPR/Cas system and the resistance gene guidance method based on the co-evolution theory of natural product and organisms in nature. Moreover, the research progress of three breeding methods for herbicide resistant crops was reviewed, including conventional breeding, transgenic breeding and CRISPR/Cas genome editing based breeding. Among them, the research progress of CIRSPR/Cas system, base editing technology, and prime editing system in cultivating herbicide resistant crops were highlighted. The main challenge faced by chemical control of weeds and herbicide resistant crops is resistant weeds and environmental safety issues, and gene escape, respectively. At present, the rapid development of genome editing technology provides new solutions and new opportunities for the development of herbicide resistant crops in the post genome era. Finally, the prospects for the future of herbicide-resistant crops were provided.

Lignin is one of the main components of cell walls and is essential for resistance to insect pests in plants. Cotton plants are damaged by aphid (Aphis gossypii) worldwide but resistant breeding is undeveloped due to scarce knowledge on resistance genes and the mechanism. This study reported a lignin biosynthesis-related gene identified in the F₂ population derived from the cross between cotton cultivars Xinluzao 61 (resistant to aphid) and Xinluzao 50 (susceptible to aphid). A quantitative trait locus was mapped on chromosome D04 with a logarithm of odds (LOD) score of 5.99 and phenotypic effect of 27%. RNA-seq analysis of candidate intervals showed that the expression level of GH_D04G1418 was higher in the resistant cultivar than in the susceptible cultivar. This locus is close to AtLAC4 in the phylogenetic tree and contains a conserved laccase domain. Hence, it was designated GhLAC4-3. Silencing of GhLAC4-3 in Xinluzao 61 via virus-induced gene silencing (VIGS) resulted in decreased lignin content and increased susceptibility to aphids. These results suggest that GhLAC4-3 might enhance aphid resistance by regulating lignin biosynthesis in cotton.

Environmental stresses severely impair cotton production worldwide. To identify the genetic basis of, and molecular markers associated with, environmental stresses such as salt, cold and Verticillium wilt, association mapping of salt-, cold-, and disease-tolerance traits was performed in a population of 503 upland cotton accessions using 179 polymorphic SSR markers and 11,975 array-derived SNP markers. Salt and cold tolerance was evaluated via the relative germination rate (RGR) of the seeds under seven and four environments, respectively. The disease index of Verticillium wilt was investigated for two years in the field in Xinjiang. These three traits showed large variation across environments. A genome-wide association study revealed that 31, 19, and 15 SSR markers were associated with RGR-Salt (the relative germination rates of seeds under salt stress), RGR-Cold (the relative germination rates of seeds under cold stress), and DIV (the disease index of Verticillium wilt), respectively. Six SNPs in seven environments and two SNPs in BLUP (best linear unbiased prediction) results were associated with RGR-Salt, and the phenotypic variance explained ranged from 3.96 to 5.00%. Two SNPs (i02237Gh, i02243Gh) on D01 were concluded to be stable genetic loci associated with RGR-Salt. A total of 223 genes were found in a candidate gene interval (D01, 37771–1942912). Of these four genes, GhPIP3A, GhSAG29, GhTZF4, and GhTZF4a, showed expression changes in sensitive and tolerant genotype accessions under salt stress, and were assigned as candidate genes associated with RGR-Salt. This study revealed the genetic basis of stress resistance in upland cotton and will facilitate stress-resistance breeding in cotton.