Genomic characterization of multi-parental populations of sorghum and rice

This thesis describes research work performed at the University of Illinois at Urbana- Champaign (UIUC) and the International Rice Research Institute (IRRI) on genetic analysis of two important cereal crops, sorghum and rice. Research presented in chapters 1 and 2 was performed at UIUC under the supervision of Dr. Patrick J. Brown, and research presented in chapter 3 was performed at IRRI under the supervision of Dr. Kenneth L. McNally. Sorghum is the world’s fifth most important cereal crop and is critical for food security in semi-arid regions. Chapter 1 describes the generation of genetic linkage maps for eight sorghum recombinant inbred line (RIL) populations using genotyping-by-sequencing (GBS) data. In this work, 1626 RILs from eight biparental populations were genotyped using a modified GBS protocol with Y-adapters. For SNP calling used the TASSEL5 GBS pipeline, and genetic linkage maps were produced using ASMap, an R package that implements MSTMap algorithm. Chapter 2 describes the skim (~5X) sequencing of 240 bioenergy sorghum genomes, using a whole-genome sequencing library preparation protocol that was developed in-house and is cost- effective and less labor-intensive than existing methods. Rice is a staple food for most of the world’s population, and 90% of the rice produced globally is used for human consumption. Rice production requires a significant amount of fresh water. Drought is one of the major abiotic stresses of rice and is responsible for up to 40% yield loss of total world production, annually. Modern rice cultivars have lost most of their genetic diversity, and the use of crop wild relatives (CWRs) in breeding needs to be explored. IRRI has developed four backcross introgression line (BIL) populations using wild progenitors of Asian cultivated rice as donor parents. Chapter 3 describes the genotype data analysis of these four populations and phenotyping of a subset of each of the four populations under well-watered and managed water stress conditions. This field experiment was conducted at IRRI in the Philippines during the 2018 dry season. Analysis of phenotype data collected for the subsets indicates considerable genotypic variation, and researchers have shown interest in using these lines in their breeding programs. A total of sixteen lines, four from each population, were selected based on the 2018 DS and are being tested at IRRI for physiological traits.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Crop Sciences

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2020

Author dc:creator

• Hirannaiah, Pradeepa

Contributors dc:contributor

• Brown, Patrick J
• Juvik, John A
• Hudson, Matthew E
• Moose, Stephen P
• McNally, Kenneth L

• Rice CWRs
• Drought tolerance in rice CWR BILs
• Sorghum WGS library prep

Statement dc:rights

• Copyright 2019 Pradeepa Hirannaiah

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/106337

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/106337