Genetic dissection of seedling vigour in a diverse panel from the 3,000 Rice (Oryza sativa L.) Genome Project

Kai Chen,Jian-Long Xu,Qiang Zhang,Chun-Chao Wang,Zhi-Kang Li,Lai-Yuan Zhai,Tian-Qing Zheng,Yi-Jun Jiang,Zhi-Xia Liu

doi:10.1038/s41598-019-41217-x

Abstract

Seedling vigour (SV) is important for direct seeding rice (Oryza sativa L.), especially in a paddy-direct seeding system, but the genetic mechanisms behind the related traits remain largely unknown. Here, we used 744 germplasms, having at least two subsets, for the detection of quantitative trait loci (QTLs) affecting the SV-related traits tiller number, plant height, and aboveground dry weight at three sampling stages, 27, 34, and 41 d after sowing. A joint map based on GAPIT and mrMLM produced a satisfying balance between type I and II errors. In total, 42 QTL regions, containing 18 (42.9%) previously reported overlapping QTL regions and 24 new ones, responsible for SV were detected throughout the genome. Four QTL regions, qSV1a, qSV3e, qSV4c, and qSV7c, were delimited and harboured quantitative trait nucleotides that are responsible for SV-related traits. Favourable haplotype mining for the candidate genes within these four regions, as well as the early SV gene OsGA20ox1, was performed, and the favourable haplotypes were presented with donors from the 3,000 Rice Genome Project. This work provides new information and materials for the future molecular breeding of direct seeding rice, especially in paddy-direct seeding cultivation systems.

Highlights

With economic and social development, cultivating systems for rice (Oryza sativa L.) production have changed
The growth of rice is different for seedlings under transplanting rice (TTR) and paddy direct seeding (PDS) conditions owing to the transplanting recovery procedure
The distribution range of tiller number (TN) and plant height (PH) almost remained almost unchanged from sampling stages A to C

Summary

Introduction

With economic and social development, cultivating systems for rice (Oryza sativa L.) production have changed. DSR can significantly reduce water consumption and labour requirements, while increasing system productivity and resource use efficiency[2]. It can reduce greenhouse gas emissions during rice cultivation[3]. The late SV (LSV), 28 d after sowing (DAS) is more important for the population type and final grain yield, especially in PDS. This is similar to the rice in the TTR cultivating system. A multi-locus random-single nucleotide polymorphism (SNP)-effect mixed linear model package, named mrMLM, was recently developed to overcome this shortcoming[24]

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