17 Iqra Sajjad Muhammad Saeed Ghulam Sarwar Journal of Animal and Plant Sciences JAPS 20262026 36 6 1018-7081 https://doi.org/10.36899/JAPS.2026.6.0151 <p style="text-align: justify;">Cotton (<em>Gossypium hirsutum</em>&nbsp;L.) is a significant agricultural crop, primarily grown commercially for its natural fiber, while cottonseed is further processed to produce vegetable oil as a valuable by-product. This study aimed to conduct a genome-wide association study in cotton (<em>Gossypium hirsutum</em>&nbsp;L.) for morphology, cotton leaf curl virus disease index, leaf photosynthetic pigments content, and seed cotton yield under field conditions. One hundred cotton genotypes were planted under randomized complete block design in the field during 2021, 2022, and 2023 and data were collected for morphological traits, leaf photosynthetic pigment content, cotton leaf curl disease index (%), and yield attributes. Significant differences were observed among cotton genotypes for all studied traits. Plant height ranged from 80-190 cm, 64-172.67 cm, 110-245 cm, respectively, whereas, seed cotton yield per plant ranged from 9.12-262.83 g, 57.42-109.89 g, 18.78-201.6 g during 2021, 2022, 2023, respectively. Seed cotton yield per plant showed a significant positive correlation (<em>P</em>&nbsp;<u>&lt;</u>&nbsp;0.01) with the number of nodes, number of sympodial branches, number of bolls per plant, and boll weight. Cotton genotypes with stable and lower values of chlorophyll&nbsp;<em>a</em>&nbsp;and total chlorophyll had significantly higher seed cotton yield per plant. This suggested that under changing environmental conditions, cotton genotypes with optimal vegetative growth would produce sustainable seed cotton yield per plant. Cotton genotypes were genotyped using 62 polymorphic simple sequence repeat markers. Six SSR markers were found significantly associated (<em>P</em>&nbsp;<u>&lt;</u>&nbsp;0.001;&nbsp;<em>R</em><em>²</em>&nbsp;Marker&nbsp;<u>&gt;</u> 10%) with seed cotton yield per plant. These markers were BNL-150 (06D), BNL-3398 (03A), BNL-3638 (08D), CIR-253 (05A), NAU-2336 (02D) and NAU-2579 (10D); whereas, 8 SSR markers BNL-3398 (03A), BNL-4015 (04A), BNL-2609 (05A), CIR-253 (05A), BNL-150 (06D), BNL-1513 (08D), BNL-3638 (08D), and BNL-3779 (09A) were associated with plant morphology, chlorophyll contents and yield traits simultaneously under 2 or 3 years phenotypic data. These identified simple sequence repeat markers would accelerate marker-assisted breeding efforts to develop elite cotton cultivars for sustainable cotton production under changing environments.</p> cotton; genome-wide association study; photosynthetic pigments; simple sequence repeats (SSRs); sustainable cotton production Pakistan Agricultural Scientists Forum https://thejaps.org.pk/AbstractView.aspx?mid=2026-JAPS-633