QTL Hotspots for Early Vigor and Related Traits under Dry Direct-Seeded System in Rice (Oryza sativa L.).

Uma M Singh,Shilpi Dixit,M Nagamallika Devi,P Janaki Ramayya,Arvind Kumar,K Anitha Raman,Shailesh Yadav

doi:10.3389/fpls.2017.00286

Abstract

Strong seedling vigor is desirable trait in dry direct-seeded rice (DSR) for enhancing crop establishment and the ability to compete against weeds. A set of 253 BC3F4 lines derived from cross between Swarna and Moroberekan was phenotyped for early vigor (EV) and 8 related traits viz., early uniform emergence (EUE), shoot length (SHL), stem length (SL), shoot fresh weight (SFW), total fresh weight (TFW), shoot dry weight (SDW), total dry weight (TDW), and root dry weight (RDW). Composite interval mapping analysis using genotypic data from 194 SNP markers identified six genomic regions associated with traits on chromosomes 3, 4, 5, and 6 with phenotypic variance ranging from 2.5 to 18.6%. Among them 2 QTL regions; one on chr3 (id3001701-id300833) and the other on chr5 (wd5002636-id5001470) were identified as QTL hotspots A and B respectively and expressed consistently in field as well as glasshouse condition. The majority of QTLs identified for early vigor, and related traits were clustered in the QTL hotspots A (qEV3.1, qEUE3.1, qSHL3.1, qSL3.1, qSFW3.1, qTFW3.1, qRDW3.1) and QTL hotspot B (qEV5.1, qEUE5.1, qSHL5.1, qSL5.1, qSFW5.1, qSDW5.1, qTDW5.1). Ten putative candidate genes viz., 1-alpha-amylase precursor, 2-glutamate decarboxylase, 1-ethylene-insensitive 3, 3-expansin precursor, and 3-phenylalanine ammonia-lyase associated with the target traits were identified in the selected QTL regions. Mutations were identified in the coding region of alpha-amylase precursor and ethylene-insensitive 3 gene between the parents which can be utilized in marker assisted breeding. Trait relationships among the agro-physiological traits were examined to select the best genotypes for the given traits for use in future breeding programs.

Highlights

Rice is the most grown cereal worldwide and is the major food for more than one-third of the world’s population
Mixed model analysis of data from the field trials conducted during the wet seasons of 2014 and 2015 revealed significant differences between the entries for plant height and grain yield
Analysis of variance of the physiological traits measured on 8 days after sowing (DAS) and 21 DAS for the glasshouse trial indicated that the entries differed significantly for most traits except shoot dry weight (SDW) on both measurement days and root dry weight (RDW) at 21 DAS (Supplementary Table 2)

Summary

Introduction

Rice is the most grown cereal worldwide and is the major food for more than one-third of the world’s population. Reports have suggested that DSR has the advantage of input water saving from 35 to 57%, low labor costs, and low methane emission (Sharma et al, 2002; Singh et al, 2002; Sidhu et al, 2014). Given these factors, a shift from TPR to DSR in the rice cultivation system is deemed necessary. Dry DSR is more advantageous over wet and water DSR as it consumes less water, less labor intensive, saves time in sowing the crop, has low methane emission (Chauhan, 2012; Joshi et al, 2013), and is better suited to undertake mechanized agricultural operations

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