Discovery of new genetic determinants of morphological plasticity in rice roots and shoots under phosphate starvation using GWAS

Plasticity QTLs specifically contribute to the genotype × water availability interaction in maize

KEY MESSAGE

Multi-trial genome wide association study of plasticity indices allow to detect QTLs specifically involved in the genotype x water availability interaction. Concerns regarding high maize yield losses due to increasing occurrences of drought events are growing, and breeders are still looking for molecular markers for drought tolerance. However, the genetic determinism of traits in response to drought is highly complex and identification of causal regions is a tremendous task. Here, we exploit the phenotypic data obtained from four trials carried out on a phenotyping platform, where a diversity panel of 254 maize hybrids was grown under well-watered and water deficit conditions, to investigate the genetic bases of the drought response in maize. To dissociate drought effect from other environmental factors, we performed multi-trial genome-wide association study on well-watered and water deficit phenotypic means, and on phenotypic plasticity indices computed from measurements made for six ecophysiological traits. We identify 102 QTLs and 40 plasticity QTLs. Most of them were new compared to those obtained from a previous study on the same dataset. Our results show that plasticity QTLs cover genetic regions not identified by QTLs. Furthermore, for all ecophysiological traits, except one, plasticity QTLs are specifically involved in the genotype by water availability interaction, for which they explain between 60 and 100% of the variance. Altogether, QTLs and plasticity QTLs captured more than 75% of the genotype by water availability interaction variance, and allowed to find new genetic regions. Overall, our results demonstrate the importance of considering phenotypic plasticity to decipher the genetic architecture of trait response to stress.

Genome-wide association study reveals useful QTL and genes controlling the fatty acid composition in rice bran oil using Vietnamese rice landraces

In rice (Oryza sativa L.), rice bran contains valuable nutritional constituents, such as high unsaturated fat content, tocotrienols, inositol, γ-oryzanol, and phytosterols, all of which are of nutritional and pharmaceuticals interest. There is now a rising market demand for rice bran oil, which makes research into their content and fatty acid profile an area of interest. As it is evident that lipid content has a substantial impact on the eating, cooking, and storage quality of rice, an understanding of the genetic mechanisms that determine oil content in rice is of great importance, equal to that of rice quality. Therefore, in this study, we performed a genome-wide association study on the composition and oil concentration of 161 Vietnamese rice varieties. Five categories of fatty acids in rice bran were discovered and the bran oil concentration profile in different rice accessions was identified. We also identified 229 important markers related to the fatty acid composition of bran oil, distributed mainly on chromosomes 1 and 7. Seven quantitative trait loci and five potential genes related to unsaturated fatty acid content were detected, including OsKASI, OsFAD, OsARF, OsGAPDH, and OsMADS29. These results provide insights into the genetic basis of rice bran oil composition, which is pivotal to the metabolic engineering of rice plants with desirable bran oil content through candidate genes selection.

Genome wide association studies for acid phosphatase activity at varying phosphorous levels in Brassica juncea L

Acid phosphatases (Apases) are an important group of enzymes that hydrolyze soil and plant phosphoesters and anhydrides to release Pi (inorganic phosphate) for plant acquisition. Their activity is strongly correlated to the phosphorus use efficiency (PUE) of plants. Indian mustard (Brassica juncea L. Czern & Coss) is a major oilseed crop that also provides protein for the animal feed industry. It exhibits low PUE. Understanding the genetics of PUE and its component traits, especially Apase activity, will help to reduce Pi fertilizer application in the crop. In the present study, we evaluated 280 genotypes of the diversity fixed foundation set of Indian mustard for Apase activity in the root (RApase) and leaf (LApase) tissues at three- low (5µM), normal (250µM) and high (1mM) Pi levels in a hydroponic system. Substantial effects of genotype and Pi level were observed for Apase activity in both tissues of the evaluated lines. Low Pi stress induced higher mean RApase and LApase activities. However, mean LApase activity was relatively more than mean RApase at all three Pi levels. JM06016, IM70 and Kranti were identified as promising genotypes with higher LApase activity and increased R/S at low Pi. Genome-wide association study revealed 10 and 4 genomic regions associated with RApase and LApase, respectively. Annotation of genomic regions in the vicinity of peak associated SNPs allowed prediction of 15 candidates, including genes encoding different family members of the acid phosphatase such as PAP10 (purple acid phosphatase 10), PAP16, PNP (polynucleotide phosphorylase) and AT5G51260 (HAD superfamily gene, subfamily IIIB acid phosphatase) genes. Our studies provide an understanding of molecular mechanism of the Apase response of B. juncea at varying Pi levels. The identified SNPs and candidate genes will support marker-assisted breeding program for improving PUE in Indian mustard. This will redeem the crop with enhanced productivity under restricted Pi reserves and degrading agro-environments.

Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway

Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.

Prospects of genetics and breeding for low-phosphate tolerance: an integrated approach from soil to cell

Improving phosphorus (P) crop nutrition has emerged as a key factor toward achieving a more resilient and sustainable agriculture. P is an essential nutrient for plant development and reproduction, and phosphate (Pi)-based fertilizers represent one of the pillars that sustain food production systems. To meet the global food demand, the challenge for modern agriculture is to increase food production and improve food quality in a sustainable way by significantly optimizing Pi fertilizer use efficiency. The development of genetically improved crops with higher Pi uptake and Pi-use efficiency and higher adaptability to environments with low-Pi availability will play a crucial role toward this end. In this review, we summarize the current understanding of Pi nutrition and the regulation of Pi-starvation responses in plants, and provide new perspectives on how to harness the ample repertoire of genetic mechanisms behind these adaptive responses for crop improvement. We discuss on the potential of implementing more integrative, versatile, and effective strategies by incorporating systems biology approaches and tools such as genome editing and synthetic biology. These strategies will be invaluable for producing high-yielding crops that require reduced Pi fertilizer inputs and to develop a more sustainable global agriculture.

Genomic regions and candidate genes selected during the breeding of rice in Vietnam

Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica‐5 group. Here, we leveraged that strong differentiation and 672 native rice genomes to identify genomic regions and genes putatively selected during the breeding of rice in Vietnam. We identified significant distorted patterns in allele frequency (XP‐CLR) and population differentiation scores (F_ST) resulting from differential selective pressures between native subpopulations, and later annotated them with QTLs previously identified by GWAS in the same panel. We particularly focussed on the outlying Indica‐5 subpopulation because of its likely novelty and differential evolution, where we annotated 52 selected regions, which represented 8.1% of the rice genome. We annotated the 4576 genes in these regions and selected 65 candidate genes as promising breeding targets, several of which harboured alleles with nonsynonymous substitutions. Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.

Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale)

Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

BACKGROUND

Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.

RESULTS

We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width.

CONCLUSIONS

We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.