Detection of a novel locus involved in non-seed-shattering behaviour of Japonica rice cultivar, Oryzasativa 'Nipponbare'

Genetic Diversity of Weedy Rice and Its Potential Application as a Novel Source of Disease Resistance

Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowed it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for noxious agricultural weed management but also for the transfer of weedy rice traits to cultivated rice. Molecular studies of weedy rice using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and whole-genome sequence have shown great genetic variations in weedy rice populations globally. These variations are evident both at the whole-genome and at the single-allele level, including Sh4 (shattering), Hd1 (heading and flowering), and Rc (pericarp pigmentation). The goal of this review is to describe the genetic diversity of current weedy rice germplasm and the significance of weedy rice germplasm as a novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual loci that control important traits can be of great target to rice breeders.

Detection of novel loci involved in non-seed-shattering behaviour of an indica rice cultivar, Oryza sativa IR36

Asian rice (Oryza sativa) was domesticated from O. rufipogon, and reduced seed-shattering behaviour was selected to increase yields. Two seed-shattering loci, qSH3 and sh4, are involved in reducing seed shattering in both japonica and indica rice cultivars, while qSH1 and qCSS3 are likely specific to japonica cultivars. In indica cultivars, qSH3 and sh4 fail to explain the degree of seed shattering, as an introgression line (IL) of O. rufipogon W630 carrying domesticated alleles at qSH3 and sh4 still showed seed shattering. Here we analysed differences in seed-shattering degree between the IL and the indica cultivar IR36. The values for grain detachment in the segregating population between the IL and IR36 were continuous. Based on QTL-seq analysis using the BC₁F₂ population between the IL and IR36, we detected two novel loci, qCSS2 and qCSS7 (QTLs for the Control of Seed Shattering in rice on chromosomes 2 and 7), which contributed to the reduced seed shattering in IR36. We further investigated the genetic interaction of qCSS2 and qCSS7 under the presence of qSH3 and sh4 mutations in O. rufipogon W630 and found that IL carrying IR36 chromosomal segments covering all four loci are required to explain seed-shattering degree in IR36. Since qCSS2 and qCSS7 were not detected in previous studies on seed shattering in japonica, their control may be specific to indica cultivars. Therefore, they are important to understanding the history of rice domestication as well as to adjusting the seed-shattering degree of indica cultivars to maximise their yield.

Seed Shattering: A Trait of Evolutionary Importance in Plants

Seed shattering refers to the natural shedding of seeds when they ripe, a phenomenon typically observed in wild and weedy plant species. The timing and extent of this phenomenon varies considerably among plant species. Seed shattering is primarily a genetically controlled trait; however, it is significantly influenced by environmental conditions, management practices and their interactions, especially in agro-ecosystems. This trait is undesirable in domesticated crops where consistent efforts have been made to minimize it through conventional and molecular breeding approaches. However, this evolutionary trait serves as an important fitness and survival mechanism for most weeds that utilize it to ensure efficient dispersal of their seeds, paving the way for persistent soil seedbank development and sustained future populations. Weeds have continuously evolved variations in seed shattering as an adaptation under changing management regimes. High seed retention is common in many cropping weeds where weed maturity coincides with crop harvest, facilitating seed dispersal through harvesting operations, though some weeds have notoriously high seed shattering before crop harvest. However, high seed retention in some of the most problematic agricultural weed species such as annual ryegrass (Lolium rigidum), wild radish (Raphanus raphanistrum), and weedy amaranths (Amaranthus spp.) provides an opportunity to implement innovative weed management approaches such as harvest weed seed control, which aims at capturing and destroying weed seeds retained at crop harvest. The integration of such management options with other practices is important to avoid the rapid evolution of high seed shattering in target weed species. Advances in genetics and molecular biology have shown promise for reducing seed shattering in important crops, which could be exploited for manipulating seed shattering in weed species. Future research should focus on developing a better understanding of various seed shattering mechanisms in plants in relation to changing climatic and management regimes.

Direct identification of a mutation in OsSh1 causing non-shattering in a rice (Oryza sativa L.) mutant cultivar using whole-genome resequencing

Loss of seed shattering has been regarded as a key step during crop domestication. Mutagenesis contributes to the development of novel crop cultivars with a desired seed-shattering habit in a relatively short period of time, but also to uncovering the genetic architecture of seed shattering. 'Minamiyutaka', a non-shattering indica rice cultivar, was developed from the easy-shattering cultivar 'Moretsu' by mutation breeding via gamma-ray irradiation. In present study, we observed significant differences in shattering habit, breaking tensile strength, and abscission zone structure between 'Moretsu' and 'Minamiyutaka'. Whole-genome mutation analysis of 'Minamiyutaka' newly identified a 13-bp deletion causing defective splicing in exon 3 of the OsSh1 gene which has previously been referred to as a candidate for controlling seed shattering. Using CRISPR/Cas9 gene editing, we demonstrated that loss-of-function mutation in OsSh1 causes non-shattering in rice. Furthermore, gene expression analysis suggests that OsSh1 may function downstream of qSH1, a known key gene involved in abscission zone differentiation. Nucleotide diversity analysis of OsSh1 in wild rice accessions and cultivars revealed that OsSh1 has been under strong selection during rice domestication, and a missense mutation might have contributed to the reduction of seed shattering from the wild progenitors to cultivated rice.