Kernel morphometric traits in hexaploid wheat (Triticum aestivum L.) are modulated by intricate QTL  QTL and genotype  environment interactions Ramya Prashant a , Narendra Kadoo a , Charushila Desale a , Prajakta Kore a , Harcharan Singh Dhaliwal b,1 , Parveen Chhuneja b , Vidya Gupta a, * a Plant Molecular Biology Group, Biochemical Sciences Division, National Chemical Laboratory, Pune 411008, Maharashtra, India b School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana 141004, Punjab, India article info Article history: Received 17 January 2012 Received in revised form 29 April 2012 Accepted 7 May 2012 Keywords: Kernel size and shape Stable QTLs Epistatic QTLs Genotype  environment interactions abstract Wheat kernel size and shape influence its flour yield and market price. A hexaploid wheat population of 185 recombinant inbred lines was evaluated for five kernel morphometric traits namely, 1000-kernel weight, kernel length, width, lengthewidth ratio and factor form density in two diverse agro-climatic regions in India in five to eight yearelocation combinations. Additive main effects and multiplicative interaction analysis revealed significant contributions from genotype (G) and genotype  environment (G  E) effects for these traits. Quantitative trait locus (QTL) analysis by composite interval mapping (CIM) was performed using a linkage map of 251 SSR markers and 59 QTLs distributed on 16 chromo- somes were identified. The majority of the QTLs were located on the D genome (44.07%) and the homeologous chromosomes of Group 2 (38.98%). Stable QTLs detected in three or more yearelocation combinations were identified for four traits. Multi-trait CIM showed 10 chromosomal regions harboring putative pleiotropic loci. Complexity in the genetic effects was further revealed by QTL analysis based on mixed-linear model that indicated 19 QTLs with significant individual effects (main-effect QTLs) and 14 QTL  QTL interactions. Five of these nineteen main-effect QTLs and one of the fourteen QTL  QTL interactions showed environmental influence. Ó 2012 Elsevier Ltd. All rights reserved. 1. Introduction Wheat breeding programs worldwide aim at developing wheat cultivars with superior agronomic and flour yield along with improved end-use quality. Kernel morphometric traits are one of the important yield and quality components in wheat. The modern automated industrial roller mills demand wheat grains with specific quality characteristics to ensure maximum flour yield. Previous studies have reported correlation between milling yield and kernel size and shape (Berman et al., 1996; Breseghello and Sorrells, 2006). Berman et al. (1996) suggested image analysis of whole grains for the noninvasive prediction of milling yield. In contrast, kernel morphology and flour yield evaluated in 24 wheat cultivars were not significantly correlated in the studies performed by Schuler et al. (1995). Recently, the use of the single kernel characterization system (SKCS) to record kernel size, hardness and shape in terms of kernel diameter has been recommended to regulate the roller-milling process (Wheat and Flour Testing Methods, 2008). The appearance of a wheat sample can influence its market price, with bold and lustrous grains claiming consumer preference both at household and industrial levels. During varietal development in India, breeding material is evaluated for grain appearance score taking into consideration grain size, shape, soundness, color and luster (Gupta et al., 2008). Since wheat kernel size and shape can influence its market value, understanding the genetic architecture of kernel morphometric traits can help in developing wheat varieties with better commercial potential. Various cytogenetic and molecular marker-based approaches revealed quantitative trait loci (QTLs) for kernel morphometric traits (Ammiraju et al., 2004; Breseghello and Sorrells, 2006, 2007; Campbell et al., 1999; Dholakia et al., 2003; Gegas et al., 2010; Manickavelu et al., 2011; Ramya et al., 2010; Sun et al., 2009, 2010; Tsilo et al., 2010). Genetic analysis of kernel weight has been performed individually (Ammiraju et al., 2001; Groos et al., 2003; Kumar et al., 2006; Mir et al., 2008) or in terms of 1000- kernel weight (TKW), an agronomic yield component (Neumann et al., 2011; Wang et al., 2009). These previous studies together suggested genome-wide distribution of kernel morphometric trait * Corresponding author. Tel.: þ91 20 25902237; fax: þ91 20 25902648. E-mail address: vs.gupta@ncl.res.in (V. Gupta). 1 Present address: Akal School of Biotechnology, Eternal University, Baru Sahib via Rajgarh, Sirmour 173101, Himachal Pradesh, India. Contents lists available at SciVerse ScienceDirect Journal of Cereal Science journal homepage: www.elsevier.com/locate/jcs 0733-5210/$ e see front matter Ó 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.jcs.2012.05.010 Journal of Cereal Science 56 (2012) 432e439