agronomy Article Identification of Associations between SSR Markers and Quantitative Traits of Maize (Zea mays L.) Jan Bocianowski 1, * , Kamila Nowosad 2 , Barbara Wróbel 3 and Piotr Szulc 4   Citation: Bocianowski, J.; Nowosad, K.; Wróbel, B.; Szulc, P. Identification of Associations between SSR Markers and Quantitative Traits of Maize (Zea mays L.). Agronomy 2021, 11, 182. https://doi.org/10.3390/agronomy 11010182 Received: 2 December 2020 Accepted: 15 January 2021 Published: 19 January 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Department of Mathematical and Statistical Methods, Pozna ´ n University of Life Sciences, Wojska Polskiego 28, 60-637 Pozna ´ n, Poland 2 Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Grunwaldzki 24A, 53-363 Wroclaw, Poland; kamila.nowosad@upwr.edu.pl 3 Department of Grasslands, Institute of Technology and Life Sciences, Falenty, Hrabska 3, 05-090 Raszyn, Poland; b.wrobel@itp.edu.pl 4 Department of Agronomy, Pozna´ n University of Life Sciences, Dojazd 11, 60-632 Pozna ´ n, Poland; piotr.szulc@up.poznan.pl * Correspondence: jan.bocianowski@up.poznan.pl; Tel.: +48-61-8487-143 Abstract: Microsatellite or simple sequence repeat (SSR) markers have wide applicability for ge- netic analysis in crop plant improvement strategies. Marker-assisted selection is an important tool for plant breeders to increase the efficiency of a breeding process, especially for multigenic traits, highly influenced by the environment. In this paper, the relationships between SSR markers and 26 quantitative traits of hybrid maize varieties (Zea mays L.) were analyzed. Association analyses were performed based on 30 SSR primers in a set of thirteen hybrid maize varieties. A total of 112 SSR markers were detected in these genotypes. The number of alleles per locus ranged from 1 to 17, with the average number of alleles per locus equal to 3.7. The number of molecular markers associated with observed traits ranged from 1 (for the number of kernels in row, ears weight and fresh weight of one plant) to 14 (for damage of maize caused by P. nubilalis) in 2016 as well as from 1 (for soil plant analysis development—SPAD, the number of grains in ear and fresh weight of one plant) to 12 (for carotenoids content) in 2017. The sum of statistically significant associations between SSR markers and at least one trait was equal to one hundred sixty in 2016 as well as one hundred twenty-five in 2017. Marker trait associations (MTAs) were found on the basis of regression analysis. The proportion of the total phenotypic variances of individual traits explained by the marker ranged from 24.4% to 77.7% in the first year of study and from 24.3% to 77.9% in 2017. Twenty-two SSR markers performed a significant effect on at least one tested trait in both years of experiment. The three markers (phi021/4, phi036/3, and phi061/2) can be a good tool in marker-assisted selection because they allow simultaneous selection for multiple traits in both years of study, such as the number of kernels in row and the number of grains in ear (phi021/4), the number of plant after germination, the number of plants before harvest, and the number of ears (phi036/3), as well as moisture of grain and length of ears (phi061/2). Keywords: maize; microsatellite markers; quantitative traits; regression 1. Introduction Maize (Z. mays L.) belongs to the group of crops in which significant breeding progress has been observed in recent years. It is manifested not only by a large number of new hybrid varieties but also by changes in the selection of different types of breeding [1]. All maize varieties offered for cultivation are hybrid varieties, characterized by exuberance, high vigor, and good alignment [2]. Progress in maize breeding is very high, and the average period of use of varieties in production rarely lasts more than 10 years [1,3]. New maize varieties are characterized by better tolerance to a cold weather and a vigor of initial growth, as well as higher yield and lower moisture content during harvesting [4–6]. Agronomy 2021, 11, 182. https://doi.org/10.3390/agronomy11010182 https://www.mdpi.com/journal/agronomy