Identification and Molecular analysis of the Y-specific CpMp gene controlling long male peduncles in papaya

Papaya is a fruit crop possessing XY sex chromosomes. The development of long 
male peduncles (Mp) is pivotal for the evolutionary transition from gynodioecy to 
dioecy. The gene, CpMp, which controls peduncle length, is one of the four genes 
contributing to the evolution of stage 3 sex chromosomes in papaya. We identified a 
Y-specific SVP paralog, CpSVP-Yp, as a candidate gene for CpMp through 
comparative genomic analyses and functional validation by complementation tests. 
CpMp promotes peduncle elongation by directly activating CpYUC6, an auxin 
biosynthesis gene, thereby increasing IAA levels. Elevated IAA in turn enhance GA, 
triggering expression of the GA stimulated gene CpGASA6, which drives cell division 
and elongation. Overexpression CpGASA6 confirmed its role in peduncle growth but 
revealed a feedback inhibition on IAA biosynthesis. Two upstream regulators of 
CpMp were identified, CpTRAB1, a positive regulator repressed by GA, and 
CpGATA8, a negative regulator upregulated by CpMp, forming two feedback loops. 
Notably, male trees produce 400 times more pollen than hermaphrodites, offering a 
clear fitness advantage. In papaya, three genes - two sex determination genes and this 
long male peduncle gene, are essential for the establishment of dioecy and the 
initiation of sex chromosome evolution. These findings fill a major gap in 
understanding papaya sex chromosome evolution and offer valuable genetic resources 
for papaya improvement.