Rice adaptation to high temperatures at flowering stage and to direct-seeding

Sakhale, Sandeep A

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https://hdl.handle.net/2142/115733 Copy

Description

Title

Rice adaptation to high temperatures at flowering stage and to direct-seeding

Author(s)

Sakhale, Sandeep A

Issue Date

2022-04-22

Director of Research (if dissertation) or Advisor (if thesis)

Juvik, John A

Doctoral Committee Chair(s)

Sacks, Erik J

Committee Member(s)

• Lipka, Alexander E
• Kumar, Arvind

Department of Study

Crop Sciences

Discipline

Crop Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• GWAS
• QTL
• Oryza sativa
• Rice
• DSR
• direct seeding
• heat stress

Abstract

Rice (Oryza sativa) is a staple food for half of the global population, and in Asia alone it contributes 35-75% of the total calories consumed by ~3 billion people. For most of this rice-dependent population, food security relies on the supply and distribution of rice, which is grown in diverse environments and exposed to a wide range of biotic and abiotic stresses. Due to climate change, abiotic stresses such as drought, heat, flood, and cold are expected to intensify in frequency and magnitude, negatively affecting rice yields. Therefore, to keep up with the demand for rice under expected adverse environmental conditions due to climate change, it is critical to develop varieties tolerant to drought and high temperature conditions. Keeping these problems in mind, three studies were conducted on a combined rice diversity panel consisting of Rice Diversity Panel 1 (RDP1, n=416) and the aus subset of 3k rice genome project panel (3k RGP, n=91): (1) a study of adaptation to deep sowing in Field, Pot and Test-tube experiments to improve seedling emergence and plant stand of dry direct-seeded rice (dry-DSR), (2) a genome-wide association study (GWAS) for emergence of rice sown deeply in the Field, and (3) a genome-wide association study for high-temperature tolerance at flowering stage. Dry-DSR, in contrast to the puddled transplanted rice, is potentially advantageous because it saves water, labor and energy, and is amenable to mechanization. However, seedling establishment under dry-DSR is especially challenging because moisture may be limiting unless the seeds are sown deeply (e.g., 8 cm). However, rice is generally vulnerable to deep sowing and hypoxic conditions due to excess moisture at germination, resulting in poor plant stands under dry-DSR and posing a significant challenge to farmers adopting the dry-DSR method of rice cultivation. To facilitate breeding climate-resilient cultivars that are adapted to dry-DSR, it is essential to identify the key traits, germplasm donors, quantitative trait loci (QTLs) and genes that confer high rates of emergence for deeply sown direct-seeded rice. In Chapter II, a combined diverse germplasm panel of 507 rice accessions (RDP1 and aus subset of 3K RGP), which included all the five genetic groups of rice, was evaluated in the Field, Pot, and Test-tubes for seedling establishment traits putatively associated with deep sowing tolerance in dry-DSR. The Field and Pot experiments included two sowing depth treatments: deep (8 cm) and shallow (2 cm), whereas the Test-tube experiment was conducted to rapidly assess shoot and root growth in a controlled non-stress environment. Substantial variation for seedling emergence, mesocotyl elongation, and other traits was observed among the cultivars and genetic groups. The best-performing genetic groups for the emergence and mesocotyl length under deep sowing in the field were aus, aromatic, and admixed-indica. In contrast, temperate-japonica, indica, and admixed-japonica performed poorly on average. However, in the Pot experiment, tropical and temperate-japonica were found to have a greater advantage germinating under hypoxic conditions (O2 < 0.01 mg/L) as compared to aus, indica, and aromatic, which was also reconfirmed in a controlled oxygen experiment with selected entries. Notably, the correlations between mesocotyl length (Test-tube) and emergence from deep sowing (Field) for the entire panel or within genetic groups were not as great as had been reported previously for biparental crosses, indicating that there are likely other, yet to be defined, component traits that are also important for adaptation to deep sowing. Though the Field experiment was the most informative of the three phenotyping methods for differentiating genotypes tolerant to deep sowing, the Test-tube and Pot experiments showed potential for saving time and resources via negative selection to eliminate inferior genotypes prior field evaluation. Subsequently, in Chapter III, GWAS analyses were conducted on a subset of 470 accessions from a combined diversity panel of 507 rice accessions were evaluated with 2.9 million single nucleotide polymorphisms (SNPs) for seedling emergence in the Field (shallow and deep sowing) and component traits in a Test-tube experiment. From the GWAS study for emergence from deep sowing, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6 to 17.8%. Three QTLs, qSOE1.1, qEMERG-AUS1.2, and qEMERG-AUS7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, nine were associated with emergence in aus, and six were unique to the aus genetic group. We identified twelve especially compelling candidate genes based on the functional annotation being consistent with the trait; these candidate genes primarily regulated phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. These studies provide new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep sowing tolerance in rice. The candidate genes and the marker-tagged desirable alleles identified in this study should directly benefit programs breeding for dry-DSR adaptation. Rice is sensitive to temperatures beyond 35 °C, especially during flowering stage. Understanding the genetics of heat tolerance is essential for improving rice production. A panel of 507 rice accessions (416 from RDP1 and 91 aus from 3k RGP) was evaluated for response to three weeks of heat stress (39/29 °C day/night) at the reproductive stage using controlled environment chambers and compared with non-stress control conditions (29/25 °C day/night) in a greenhouse. The number of filled and unfilled spikelets per panicle were recorded. Under heat stress, genetic groups, aus and indica were least affected for spikelet fertility and showed great genetic variation compared with other populations. Compared to the known heat-tolerant cultivar N22, we identified 45 promising donors with greater spikelet fertility under heat stress, such as Bamla Suffaid, Zhenshan 97B, Malakgit, L-202 and Bongeza. GWAS analyses using 2.9 million SNPs identified 147 highly significant SNPs for spikelet fertility (%), spikelet fertility index or number of filled spikelets, including 12 QTLs and 38 single SNP regions. Among these QTLs and single SNP regions, three were consistent with genomic regions previously reported for spikelet fertility under heat stress, including the most-documented across prior studies, qHTSF4.1. We identified 19 candidate genes that were especially interesting because they had known functions that were expected to affect flowering-stage heat-tolerance, such as abiotic stress response, gametophyte development, abscisic acid (ABA) biosynthesis, antioxidants for reactive oxygen species (ROS), and panicle exertion and grain filling. The genomic regions and candidate genes identified in this study provide novel resources for breeding to improve flowering-stage heat-tolerance in rice, which will be needed to ensure food security for humanity. The green revolution transformed rice production in the tropics and reduced poverty by breeding high-yielding indica cultivars. The current study highlights the potential value of exploiting other genetic groups of rice, especially aus, by identifying unique advantageous alleles for targeted introgression. Such efforts may facilitate the development of climate-resilient rice cultivars that maintain the high yield-potential of the green revolution under the increasing environmental stresses resulting from climate change.

Graduation Semester

2022-05

Type of Resource

Thesis

Copyright and License Information

Copyright 2022 Sandeep Sakhale

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