Cooperative Agr. Research Ctr
Non Technical Summary
The major grain crops provide most of the global caloric needs. The demand for these crops will increase in the coming decades to feed the growing world population. However, the relative yield gains of these crops have declined in recent decades, and growing these crops is becoming less profitable for US farmers. Our long-term goal is to increase the yield of these crops through optimizing shoot branching, which is a major trait that significantly influence resource use efficiency and yield. The major crops develop many branches during the vegetative and reproductive stage. Most of the branches are not productive because they senesce before flowering and producing grains. The unproductive branches compete for light and nutrients with the productive branches. The competition for resources reduces the growth and yield of the productive branches. Developing new crop types with fewer unproductive branches could improve the growth of the productive branches and increase yield. However, more knowledge of genes that regulate shoot branching is needed to develop the new crop types. Branches develop from buds in the axil of leaves. The buds either grow into branches or remain dormant. The objective of this project is to identify candidate genes that control axillary bud dormancy and outgrowth using sorghum and maize as models. The genes will be identified using two approaches, molecular and genetic. The genes will enable to improving shoot branching and increasing crop yield, and ensure sustainable and profitable crop production in the US, and satisfy the global demand for food.
Animal Health Component
Research Effort Categories
Goals / Objectives
The major goal of this project is to identify genes that control shoot branching in sorghum and maize using molecular (RNA sequencing/gene expression) and genetic (gene loci/QTL mapping) approaches. To achieve the goals of the project, we will work on the following three objectives:Objective 1: Identify genes controlling axillary bud transition from growth to dormancy. Sorghum, sweet corn, and teosinte (a wild ancestor of maize) develop axillary buds that grow into branches. We will apply shade or defoliation treatments and induce bud dormancy in these species. We will identify genes associated with growing (control) and dormant (shade or defoliated treated) buds using RNA sequencing (RNA-seq) methods.Objective 2: Identify genes controlling axillary bud transition from dormancy to growth. Some buds in sorghum, maize, and teosinte remain dormant and grow when conditions are favorable. We will identify genes associated with the dormancy to growth transition using RNA-seq.Objective 3: Identify quantitative trait loci (QTL) that control genetic variations in shoot branching. Using recombinant inbred line (RIL) populations derived from diverse sorghum genotypes selected for variations in shoot branching, we will identify QTLs associated with shoot branching.
Molecular (RNA-seq) and genetic (QTL mapping) methods will be used in this project to identify agriculturally important shoot branching genes in sorghum and maize. The RNA-seq will be conducted in four genotypes (sorghum , Maize, Sweet corn, and teosinte) and three experimental conditions: shade signals and defoliation, and growth transition of axillary buds during the reproductive stage. The RNA-seq methods for Objectives 1 and 2 are similar, and will be conducted in growth chambers and greenhouses during the vegetative and reproductive phases at PVAMU. Phenotyping of recombinant inbred lines and QTL mapping (Objective 3) will be conducted in greenhouses and field at the Texas A&M Agrilife Research Farm in Burleson County, Texas. For Objective 1, to identify the molecular mechanisms and genes regulating axillary bud dormancy in response to shade and defoliation using RNA-seq, sorghum, sweet corn, and teosinte plants will be grown in a growth chamber and treated with FR or defoliation treatments to induce dormancy of buds in the first leaf axil. The bud length in shade/defoliation and the corresponding control plants will be measured at 24 h and 48 h after the start of the treatments. Axillary buds will be sampled from the plants at 1 h, 24 h, and 48 h after the start of shade or defoliation treatments, and RNA will be extracted from the buds for RNA-seq transcriptome profiling. Samples will be collected from four biological replicates grown sequentially at different times. For objective 2, to identify genes controlling buds that transition from dormancy to growth using RNA-seq, we will grow sorghum and maize plants in the growth chamber and greenhouses. we will sample plants that transition from dormancy to growth at five sampling time points, and from four biological replicates for RNA sequencing. The RNA-seq methods, including RNA extraction from axillary buds, RNA-seq library preparation, and sequencing, are the same for Objectives 1 and 2. Raw paired-end (PE) RNA-seq reads generated from objectives 1 & 2 in FASTQ format will be aligned to the sorghum and maize reference genome. The teosinte RNA sequence reads will be aligned to the maize reference genome. The R DESeq2 package will be used to identify differentially expressed genes between treatments and the corresponding controls. Experimental methods for Objective 3: QTL mapping will be conducted in the field and greenhouses at TAMU. In the first year, we will screen the parents of 30 RIL populations to determine the range of tillering and shoot branching among those genotypes. Based on that information, two RIL populations will be selected to screen for QTL analysis of shoot branching during the vegetative and reproductive phase. Parental lines and RILs will be grown in the field and greenhouses in pots consecutively for over the duration of the study and tillering related traits will be measured for QTL mapping.