More than half of the world's population considers rice to be "food of life", as it is their primary source of calories. Milled rice is commonly consumed, which has a lesser nutritional value than brown or pigmented rice (Kushwaha 2016). Milling removes most of the minerals, protein, vitamins, and other antioxidants found in rice bran. In general, colored or pigmented rice contains higher amounts of proteins, vitamins, minerals, fibre, and phytochemicals such as tocopherols, tocotrienols, γ-oryzanols, phenolic compounds, and other phytochemicals, all of which provide numerous health benefits by supplying required nutrients. Phenolics and anthocyanins in the aleurone layer offers pigmentation on rice grains; hence, pigmented rice is consumed as brown rice (Descalsota-Empleo et al. 2019). Iron and Zinc, as well as anthocyanin-related antioxidants, are required for normal growth and development as well as living a healthy life (Goufo and Trindade 2014; Oki et al. 2002). According to Saleh et al. (2019), Fe and Zn deficiencies, malnutrition, and oxidative stress-related health problems impact more than one-third of the world's population. The deficiencies of micronutrients like Fe and Zn lead health complications like anaemia, poor cognitive development, poor immunity, low fertility, etc (Cheng et al, 2005; Bouis, 2007; Singh et al. 2007). Oxidative stress, on the other hand, is linked to a number of health issues, including stroke, psoriasis, and rheumatoid arthritis (Galli et al. 2005). Consumption of pigmented rice appears to protect against certain malignancies, according to a large body of evidences. The extracts of black and red rice demonstrates to have significant impact on inhibiting breast cancer (Ghasemzadeh et al. 2018) and anthocyanin pigments known to reduce blood cholesterol in human body (Sompong et al. 2011).
Significant raise in awareness on nutrition and health among public, the nutritional benefits of pigmented or brown rice draws public attention. Thus, the field of breeding science prioritized Fe, Zn and other anti-oxidant compounds for bio-fortification staple food sources like rice (Garg et al. 2018). Apart from micro-nutrients, protein in rice has significant role as calorie source and also for improving cooking quality of rice. Hence, improving rice varieties with significant amounts of micro-nutrients along with protein is need of the hour in the present era of nutritional security. As a prelude to bio-fortification, it is important to identify genomic regions controlling nutritional quality traits through advanced mapping approaches (Patra et al. 2020; Chattopadhyay et al. 2019a). However, few QTL controlling Fe, Zn and protein content in brown and milled rice have been reported on all 12 rice chromosomes (Sharma et al, 2020). Among these, a putative amino acid polymerase gene OsAAP6 inside QTL in chromosome 1 qPC1.1 (Peng et al. 2014) and putative gene for glutelin OsGluA2 inside QTL on chromosome 10 (qGPC10) (Yang et al, 2019) were cloned. Similarly, anthocyanin content in the pericarp of black rice was reported to regulated by Ra, Rc, Rd, Kala1, Kala3, and Kala4 genes (Winkel-Shirley 2001), of which Kala4 produces purple or black pericarp in the complementation of Kala1 and Kala3 (Maeda et al. 2014). Although brown rice is nutritionally more superior to milled rice, storability in brown rice is a serious concern due to rancidity. Moreover, brown rice has comparatively poor eating quality due to firm, chewy, hard and loose texture in cooked rice, and resulting lower acceptability by the consumers. The eating quality of red rice also makes it difficult and challenging for consumers to eat red rice on regular basis. Even biofortified rice cannot be acceptable to consumers without acceptable cooking and eating quality. Among cooking quality, amylose (AC) and gel consistency (GC) along with alkali spresding value (ASV) are considered most important. AC has been reported to be controlled mainly by waxy gene locus (Wx) which affect the cooking quality was reported on chromosome 6 and few other minor QTL for cooking quality were mapped on chromosomes 1, 3, 4, 7, 8 and 11 (Zheng et al. 2008; Tian et al. 2009). Many of these QTL were identified from bi-parental population, which restricts there transferability to other genetic backgrounds; hence, limits the practical application of these findings. Further, the variation for quantitative traits like nutritional quality should be captured by following a holistic approach instead of bi-parental mapping approach (Mather et al. 2004).
The limitations of bi-parental mapping to capture wide variation of quantitative traits may be resolved by adopting modified forms of linkage disequilibrium mapping, popularly known as genome-wide association analysis (GWAS). GWAS captures historic recombination frequency instead of parental recombination frequency for identification of genomic determinants of quantitative traits (Yu et al. 2017). Considering the existence of huge allelic diversity for nutritional traits in rice, GWAS could be the most promising strategy for simultaneous mapping of QTL for several nutritional traits with high precision (Huang and Han 2014). Hence, GWAS can be deployed for effective identification of causative alleles for rice grain nutritional traits with modest number of markers distributed over all the chromosomes.
In this milieu, a genome-wide association analysis was performed with statistically strong and diverse association panel evaluated for 17 physicochemical and nutritional traits in rice. Selected traits are considered most important in bio-fortification programs to develop mineral dense rice varieties to combat mineral malnutrition. The main objective of the study was to identify unique QTL/associated markers with traits of importance for bio-fortification and grain quality. We also aimed to identify pleiotropic QTL/marker trait association (MTA) for physicochemical and nutritional quality traits to deploy them in bio-fortification breeding programs. The results of this study have significant scope in developing strategic marker aided breeding program for bio-fortification of nutritional and grain quality traits in rice.