Characterization of popcorn temperate and tropical populations and GWAS for zeins and starch contents

Because measuring expansion volume (EV) is simple and inexpensive, popcorn breeders have developed high-quality single crosses ignoring the contents of zeins, starch, lipids, and cellular wall components in selection. However, some methods of quantification of these quality-related traits can be applied to popcorn breeding, increasing the selection efficacy for quality. The objectives of this study were assess methods of quantification of zeins and starch that can be used in popcorn breeding, characterize a temperate and a tropical populations for zeins and starch contents, and identify candidate genes for these quality-related traits. We genotyped and phenotyped 286 plants. For quantification of total zeins and zein subunits we choose the ‘lab-on-a-chip’ microfluidic electrophoresis. For quantification of starch and amylose/amylopectin we choose the Megazyme’s Amylose/Amylopectin kit assay. The temperate population has superior EV (+36%), a higher level (+32%) of the 19 kDa zein subunit, and lower levels of the 21, 22, and 27 kDa subunits (−1543, −40 and −47%, respectively). Although there are statistical differences between the two populations regarding starch, amylose, and amylose/amylopectin ratio, the differences are not significant (−2 to 8%). Six candidate genes were identified for the 19 and 22 kDa zeins, one for the 21 kDa zein, one for total zeins, two for starch, and four for amylose, with emphasis on three genes from the Z1C subfamily, coding for the 19 and 22 kDa alpha-zeins, located on chromosome 4. The evaluated quantification methods can be used in popcorn breeding programs, with the potential to revolutionize the breeding for quality. Key message The protein chip and the Amylose/Amylopectin kit assay for zein and starch quantification, respectively, can be effectively used in popcorn breeding, with the potential to revolutionize the breeding for quality. ### Competing Interest Statement The authors have declared no competing interest.