Detection of stable QTLs for grain protein content in rice (Oryza sativa L.) employing high throughput phenotyping and genotyping platforms

Krishnendu Chattopadhyay,Sushree Sibanee Sardar,Soham Ray,Nutan Moharana,Koushik Chakraborty,Sutapa Sarkar,Ananta Sarkar,Niraja Rani Patra,Avijit Das,Srigopal Sharma,Mridul Chakraborti,Bishnu Charan Marndi,Lotan Kumar Bose,Lambodar Behera,Umakanta Ngangkham,Torit Baran Bagchi

doi:10.1038/s41598-019-39863-2

Abstract

Lack of appropriate donors, non-utilization of high throughput phenotyping and genotyping platforms with high genotype × environment interaction restrained identification of robust QTLs for grain protein content (GPC) in rice. In the present investigation a BC3F4 mapping population was developed using grain protein donor, ARC10075 and high-yielding cultivar Naveen and 190 lines were genotyped using 40 K Affimetrix custom SNP array with the objective to identify stable QTLs for protein content. Three of the identified QTLs, one for GPC (qGPC1.1) and the other two for single grain protein content (qSGPC2.1, qSGPC7.1) were stable over the environments explaining 13%, 14% and 7.8% of the phenotypic variances, respectively. Stability and repeatability of these additive QTLs were supported by the synergistic additive effects of multi-environmental-QTLs. One epistatic-QTL, independent of the main effect QTL was detected over the environment for SGPC. A few functional genes governing seed storage protein were hypothesised inside these identified QTLs. The qGPC1.1 was validated by NIR Spectroscopy-based high throughput phenotyping in BC3F5 population. Higher glutelin content was estimated in high-protein lines with the introgression of qGPC1.1 in telomeric region of short arm of chromosome 1. This was supported by the postulation of probable candidate gene inside this QTL region encoding glutelin family proteins.

Highlights

Malnutrition is responsible for about 24,000 deaths per day worldwide[1]
Near Infrared (NIR) spectroscopy has been used by researchers to screen large number of germplasm for protein content in several cereals[22,23,24] and in high throughput phenotyping of breeding lines[25]
A few other QTLs reported earlier[3,6,9] were located near the present QTL qSGPC 7.1. Another putative QTL, qSGPC8.1 on chromosome 8 was located just adjacent to a QTL for grain protein content qPro-8 at 1.2 Mb position[11]. We found another putative QTL qSGPC11.1 and multi-environment trial QTL (MET-QTL) on the same position which was located very near to a QTL, qGPC-11 detected through association mapping at 4.3 Mb position with peak SNP located on gene OsAsp[153]

Summary

Introduction

Malnutrition is responsible for about 24,000 deaths per day worldwide[1]. Rice is staple food for more than half of the world population. In the present study high genetic variability governed by high protein donor followed by high throughput SNP-array based genotyping were exercised with the aim of detection of robust QTLs for grain protein content with plausible influence of epistasis and genotype × environment interaction. This investigation explored the scope of high throughput phenotyping using NIR spectroscopy to validate stable QTLs in advanced near isogenic line (NIL) population. It focused on the delineation of QTLs loci to find functional genes inside QTLs and tried to associate them with higher protein and protein fraction content in the selected stable high protein introgressed (NILs) over the environments

Methods

Results

Conclusion