Rice provides energy and nutrition to more than half of the world’s population. Breeding rice varieties with the increased levels of bioavailable micronutrients is one of the most sustainable approaches to tackle micronutrient malnutrition. So, high zinc and iron content in the grain are primary targets in rice biofortification breeding. In this study, we conducted QTL mapping using doubled haploid (DH) populations, PSBRc82 x Joryeongbyeo and PSBRc82 x IR69428, phenotyped for agronomic traits and micronutrients during two growing seasons and using genotypic information from analysis with the 6K SNP chip. A number of DH lines were identified as having high grain Zn and Fe content in polished rice. Importantly, we identified 20 QTLs for agronomic traits and 59 QTLs for a number of biofortification traits. Of the 79 QTLs, 12 were large-effect QTLs (>25% PVE), nine QTLs were consistent across seasons in either population, and one QTL was identified in both populations. Moreover, at least two QTLs were clustered in defined regions of chromosomes 1, 2, 3, 4, 5, 7 and 9. Eight epistatic interactions were detected for Cu, Mg, Na, and Zn in population 1. Furthermore, we identified several candidate genes near QTLs for grain Zn (OsNRAMP, OsNAS, OsZIP, OsYSL, OsFER, and OsZIFL family) and grain yield (OsSPL14 and OsSPL16). These new QTLs and candidate genes help to further elucidate the genetic basis for grain micronutrient concentration, and may prove useful for marker assisted breeding for this important trait.

The development of micronutrient dense rice varieties with good agronomic traits is one of the sustainable and cost-effective approaches for reducing malnutrition. Identification of QTLs for high grain Fe and Zn, yield and yield components helps in precise and faster development of high Fe and Zn rice. We carried out a three-season evaluation using IR05F102 x IR69428 derived doubledhaploid population at IRRI. Inclusive composite interval mapping was carried out using SNP markers and Best Linear Unbiased Estimates of the phenotypic traits. A total of 23 QTLs were identified for eight agronomic traits and grain Fe and Zn concentration that explained 7.2 to 22.0% PV. A QTL by environment interaction analysis confirmed the stability of nine QTLs, including two QTLs for Zn on chromosomes 5 and 12. One epistatic interaction for plant height was significant with 28.4% PVE. Moreover, five QTLs were identified for Fe and Zn that harbor several candidate genes, e.g. OsZIP6 on QTL qZn 5.1. A number of QTLs were associated with a combination of greater yield and increased grain Zn levels. These results are useful for development of new rice varieties with good agronomic traits and high grain Zn using MAS, and identification of genetic resources with the novel QTLs for grain Zn.

The lack of dietary diversity among poor communities has led to nutritional consequences, particularly zinc deficiency. An adequate intake of mineral- and vitamin-rich food is necessary for achieving and maintaining good health. Zinc is one of the micronutrients considered essential to improve human health and decrease the risk of malnutrition. Biofortification of rice through breeding is a cost-effective and sustainable strategy to solve micronutrient malnutrition. The Biofortification Priority Index prepared by HarvestPlus clearly identified several countries in Asia with an immediate need for Zn biofortification. The International Rice Research Institute (IRRI) and its national partners in target countries are making efforts to develop Zn-biofortified rice varieties. The first set of high-Zn rice varieties has been released for commercial cultivation in Bangladesh, India, the Philippines, and Indonesia. Efforts have begun to mainstream grain Zn to ensure that the Zn trait becomes an integral part of future varieties. Huge scope exists to apply advanced genomics technologies such as genomic selection and genome editing to speed up high-Zn varietal development. An efficient rice value chain for Zn-biofortified varieties, quality control, and promotion are essential for successful adoption and consumption. The development of next-generation high-Zn rice varieties with higher grain-Zn content, stacking of multiple nutrients, along with good grain quality and acceptable agronomic traits has to be fast-tracked. Healthier rice has a large demand from all stakeholders, so we need to keep up the pace of developing nutritious rice to meet the demand and to achieve nutritional security.

Biofortification of rice with improved grain zinc (Zn) content is the most sustainable and cost‐effective approach to address Zn malnutrition in Asia. Genomics‐assisted breeding using precise and consistent Zn quantitative trait loci (QTLs), genes, and haplotypes can fast‐track the development of Zn biofortified rice varieties. We conducted the meta‐analysis of 155 Zn QTLs reported from 26 different studies. Results revealed 57 meta‐QTLs with a significant reduction of 63.2% and 80% in the number and confidence interval of the Zn QTLs, respectively. Meta‐quantitative trait loci (MQTLs) regions were found to be enriched with diverse metal homeostasis genes; at least 11 MQTLs were colocated with 20 known major genes involved in the production of root exudates, metal uptake, transport, partitioning, and loading into grains in rice. These genes were differentially expressed in vegetative and reproductive tissues, and a complex web of interactions were observed among them. We identified superior haplotypes and their combinations for nine candidate genes (CGs), and the frequency and allelic effects of superior haplotypes varied in different subgroups. The precise MQTLs with high phenotypic variance, CGs, and superior haplotypes identified in our study are useful for an efficient Zn biofortification of rice and to ensure Zn as an essential component of all the future rice varieties through mainstreaming of Zn breeding.