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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #414116
Research Project: Pecan Breeding and Management of the National Collection of Carya Genetic Resources

Location: Crop Germplasm Research

Title: Alternative RNA splicing associated with pecan dichogamymunities

Author
item LI, YIYI - New Mexico State University
item SONG, JOE - New Mexico State University
item RANDALL, JENNIFER - New Mexico State University
item Chatwin, Warren
item Wang, Xinwang

Submitted to: Proceedings American Society of Horticultural Sciences
Publication Type: Abstract Only
Publication Acceptance Date: 9/23/2024
Publication Date: 9/27/2024
Citation: Li, Y., Song, J., Randall, J., Chatwin, W.B., Wang, X. 2024. Alternative RNA splicing associated with pecan dichogamymunities. Proceedings American Society of Horticultural Sciences. Honolulu,HI;23-27Sep2024.

Interpretive Summary:

Technical Abstract: Pecan (Carya illinoinensis), a North American native nut crop, exhibits two distinct flowering habits where male and female flowering occur at separate times. Trees that shed pollen before their pistillate flowers become receptive and are classified as protandrous or type 1 (recessive homozygous, pp), while those with pistillate flowers receptive before pollen shed are protogynous or type 2 (dominant heterozygous, PP/Pp). Establishing commercial pecan orchards requires planting both types of pecan cultivars to ensure optimal pollination for maximum production. To investigate the critical genes associated with pecan heterodichogamous flowering, we collected tissues from four stages (dormant buds, swollen buds, immature catkins, and immature pistils) of three genotypes (PP, Pp, and pp). RNA sequencing at 125 bp/150 bp paired-ends on the Illumina platform was conducted, and the clean and unique reads were mapped to the reference genome of 87MX3-2.11, with subsequent gene annotation. Out of 32,267 annotated genes, over 5,000 were identified through alternative splicing analysis. Here we showed three most significant genes presenting alternative splicing events were associated with dichogamy genotypes, distinguishing the pp genotypes from PP and Pp genotypes. These genes exhibited 6-18 nucleotide differences between the pp genotype and PP/Pp genotypes, potentially resulting in an altered protein product with 2-6 amino acid differences between type 1 and type 2 genotypes. This study provides evidence supporting the prevalence of alternative RNA splicing in pecan transcription. Specifically, alternative splicing patterns involving approximately 15% of annotated genes are strongly associated with pecan flowering dichogamy.