Investigating Genetic Influences on Nutritive Value of Whole Cottonseed

Abstract

Whole cottonseed (WCS), a byproduct of cotton production, is a valuable feedstuff in ruminant nutrition due to its unique combination of fat, fiber, and protein. However, the nutritive value varies significantly among cotton varieties, creating challenges for consistent feed formulation. This study aimed to investigate the genetic basis of nutritive value in WCS by identifying genetic loci associated with crude fat concentration and in vitro true digestibility using genome wide association study (GWAS). A total of 383 cotton accessions were phenotyped for crude fat concentration and in vitro true digestibility (IVTD) in two years. Crude fat concentration ranged from 10.9 to 29.0%, and IVTD from 48.5 to 63.1%. For genotyping, the CottonSNP63K array was utilized and after quality filtering, 22,983 SNP were used in the GWAS analysis with the FarmCPU model in GAPIT v3. Seventeen SNP were associated with crude fat concentration across five chromosomes (chr.), with clusters on A04 and A06. Candidate genes near these loci included AtLPEAT1, LPAT4, ELO4/HOS3, and SCP2, all involved in lipid biosynthesis and transport. For IVTD, three SNP were identified, primarily on chr. D12, with candidate genes such as LTPG15, AtBGAL10, and PPD2 which are involved in seed coat development and cell wall metabolism. Heritability estimates were low for both crude fat concentration (h2 = 0.21) and IVTD (h2 = 0.10), indicating a stronger environmental influence. To evaluate the nutritive value of WCS, a set of 20 diverse elite cotton breeding lines were used from the 2023 Regional Breeding Testing Network (RBTN) field trial entries. These 20 cotton breeding lines exhibited variation across all evaluated traits for fiber composition for NDF (34.8 to 60.1%), ADF (25.5 to 39.9%), ADL (10.4 to 18.7%), crude protein (19.6 to 27.4%), crude fat concentration (16.0 to 25.7%), and IVTD (51.6 to 59.1%). The line, Ark 1510-31, exhibited both high crude fat concentration and IVTD which is desirable for increasing the value of WCS in ruminant diets. These findings highlight the importance of considering nutritive value assessments in cotton breeding programs and highlight the RBTN as a valuable tool for integrating agronomic and nutritional evaluations. Together, these results provide a start for breeding strategies aimed at improving the consistency and quality of WCS as a livestock feed ingredient. By combining genomic insights with phenotypic evaluations, this research supports the development of cotton cultivars that meet livestock nutrition goals.