SS1 (NAL1)- and SS2-Mediated Genetic Networks Underlying Source-Sink and Yield Traits in Rice (Oryza sativa L.).

Jian-Long Xu,Yan-Ru Cui,Jia-Yang Li,Yong-Hong Wang,Zhi-Kang Li,Kai Chen,Fan Zhang,Qiang Zhang,Hong-Xuan Lin,Tian-Qing Zheng,Xiu-Qin Zhao,Yun Wang,Yuan Wu,Jauhar Ali

doi:10.1371/journal.pone.0132060

Abstract

Source leaf/sink capacity (SS) traits are important determinants of grain yield (GY) of rice. To understand the genetic basis of the SS relationship in rice, five SS and GY traits of rice were genetically dissected using two reciprocal introgression populations. Seventy-three QTL affecting the SS and GY traits were identified, most of which were detected in one of the parental genetic backgrounds (GBs). Two major QTL at bins 4.7 (SS1) and 3.12 (SS2) were associated consistently with all measured SS and yield traits in both GBs across two contrasting environments. Strong interactions between SS1/SS2 and the detected QTL led us to the discovery of genetic networks affecting the SS and GY traits. The SS1 acted as a regulator controlling two groups of downstream QTL affecting the source leaf width and grain number per panicle (GNP). SS2 functioned as a regulator positively regulating different groups of downstream QTL affecting the source leaf length, GNP, grain weight, and GY. Map-based cloning of SS1 indicates that SS1 is NAL1 involved in polar auxin/IAA transport. Different alleles at NAL1 were apparently able to qualitatively and/or quantitatively control the IAA transport from the apical meristem to different plant tissues and thus regulate those downstream loci/pathways controlling different SS traits of rice. There was a functional allele and a non-functional mutation in the parents at each of the QTL downstream of SS1 or SS2, which were detectable only in the presence of the functional allele of SS1 or SS2. Our results provided direct evidence that SS and yield traits in rice are controlled by complex signaling pathways and suggest further improvement of rice yield potential with enhanced and balanced SS relationships can be achieved by accurately manipulating allelic combinations at loci in the SS1 and SS2 mediated pathways.

Highlights

Rice (Oryza sativa L) is the staple food of most Asian people
Grain number per panicle (GNP) and grain size are the primary components of the sink capacity for photosynthetic product accumulation
We developed some insertions and deletions (InDel) and cleaved amplified polymorphic sequences (CAPS) markers in the target region designed from the reference Nipponbare and 93–11 genomic sequences (S2 Table) and determined genotypes of the recombinants with these markers

Summary

Introduction

Rice (Oryza sativa L) is the staple food of most Asian people. Rice productivity has been more than tripled in China, resulting primarily from the Green Revolution since late 1950s and the hybrid rice technology in late 1970s. Plant physiologists believe that high yield potentials of cereal crops are largely determined by enhanced and balanced relationships between the source, sink and flow of assimilates [1, 2]. Grain number per panicle (GNP) and grain size are the primary components of the sink capacity for photosynthetic product accumulation. The upper three leaves, especially the flag leaves, are the primary source of assimilate-supply for grain yield [3,4,5]. Efficient transport of assimilates from leaves and stems to developing grains is important for better grain filling and high yield [6, 7]. Characterizing genes/QTL underlying the sink-source (SS) relationship will greatly enhance our understanding of the genetic basis of yield potential in rice

Methods

Results

Conclusion