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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Research Project #444992

Research Project: Identifying Differential Gene and Protein Expression in Two Pecan Cultivars With Contrasting Nut Size, Shape, and Maturity Timing

Location: Crop Germplasm Research

Project Number: 3091-21000-046-008-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2023
End Date: Aug 31, 2024

The genes controlling the expression of nut size, nut shape, and maturity timing are unknown in pecan. These traits are critical for pecan breeding and improvement. To date, pecan breeding has followed traditional plant breeding practices of selecting superior parents based solely on observed phenotypes in the field. Pecan breeding is transitioning to incorporate genetics into the breeding process to increase the efficiency and accuracy of pecan improvement. Identifying gene networks and pathways controlling nut development and maturity timing will allow for more accurate selection in pecan breeding. This collaboration aims to identify which genes and proteins are differentially expressed between two pecan cultivars with contrasting nut size, shape, and maturity timing. The Cooperator has extensive experience in research identifying the expression of genes and proteins involved in fruit maturity in fruit trees. While pecan is commonly referred to as a nut tree, the pecan kernel is the edible seed of an inedible fruit. The Cooperator’s experience will translate well to research studying fruit size, shape, and maturity in pecan.

Two pecan cultivars, 'Mahan' and 'Tiny Tim', both originate from pecan seedlings selected by humans for valuable traits. 'Mahan' originated as a chance seedling planted about 1910 by J.M. Chestnutt of Kosciusko, Mississippi, from a pecan nut he secured from the State Fair at Jackson, Mississippi. Early advertising for 'Mahan' strongly focused on it being "the largest pecan in the world" with heavy "branch-bending" production. It tends to bear 30-60 nuts per pound and matures late (in early November) but has an extremely thin shell and medium-to-good quality kernel. 'Tiny Tim' was a native pecan growing at the upper edge of a flood basin that was selected in 1994 by the Missouri Department of Conservation for use in wetland restoration and as a wildlife food source. 'Tiny Tim' nuts are quite small, requiring hundreds of nuts to make a pound of kernels. It matures early in late August or early September and has a thick shell. Our approach was to harvest developing pecan fruit tissue in at least 14 increments throughout the expected maturity cycle of 'Tiny Tim' and 'Mahan' for two grafted clones of each accession contained on-site in the USDA Collection of Genetic Resources for Carya in College Station, TX. Developing fruits were collected from May to November, wrapped in aluminum foil, flash-frozen in liquid nitrogen, and transferred to a -80°C freezer for storage. A total of 20 time-series samples were collected for 'Mahan,' and 17 time-series samples were collected for 'Tiny Tim'. These tissue samples would be used for RNA and protein extraction and sequencing by the Cooperator. Data analysis would consist of gene and protein expression comparisons between replicate accessions at each time point and across the developmental time series. 'Mahan' has a phased, annotated genome sequence in development that will aid in identifying genes, proteins, and pathways involved in nut development and maturity. 'Tiny Tim' does not have a complete genome sequence but has about 50x coverage of genome resequencing using Illumina short reads. Long-read PacBio sequencing has decreased significantly in cost, and constructing a draft genome of 'Tiny Tim' will be considered if it will improve the resolution of the final analyses.