The genetic architecture of maize stalk strength

Authors: PEIFFER, JASON - Cornell University; Flint-Garcia, Sherry; DE LEON, NATALIA - University Of Wisconsin; McMullen, Michael; KAEPPLER, SHAWN - University Of Wisconsin; Buckler, Edward - Ed

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2013
Publication Date: 6/20/2013
Publication URL: http://handle.nal.usda.gov/10113/56904
Citation: Peiffer, J.A., Flint Garcia, S.A., De Leon, N.N., McMullen, M.D., Kaeppler, S.M., Buckler IV, E.S. 2013. The genetic architecture of maize stalk strength. PLoS One. 8(6):e67066. Available: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067066#pone-0067066-g005.

Interpretive Summary: Plant lodging in corn is the mechanical failure of a cornstalk before its grain has been harvested. This event causes major yield losses for corn production in the US, especially in areas with high winds and poorly managed soil nutrients and insect pests. A primary means to overcome this problem is the development of corn varieties with increased stalk strength. While screening germplasm collections for stronger varieties has been successful and has led to substantial crop improvement, understanding which genes are responsible for increasing stalk strength remains important to reducing plant lodging. Similarly, evaluating new diagnostic approaches to facilitate more rapid screening of larger germplasm collections using genome wide sequence data will benefit future breeding practices as well. We evaluated stalk strength in the genetically diverse nested association mapping (NAM) population and a collection of 2,453 inbred lines from the North Central Regional Plant Introduction Station. We identified numerous chromosomal regions involved in the complex genetic network regulating stalk strength. We found that diverse maize varieties contain combinations of these chromosome regions, and that no single variety possessed all the favorable variants for stalk strength. Thus, varieties with higher stalk strength may be derived by combining favorable variants from different lines into a single line by breeding and/or transgenic approaches. We also found that whole genome sequence data in these populations may be used to accurately predict stalk strength prior to its evaluation in the field. This may facilitate future screening of larger collections of germplasm without expending the resources for field testing all the corn varieties. These results may be used by corn breeders and geneticists to improve stalk strength and will further secure future grain yields.

Technical Abstract: Stalk strength is an important trait in maize (Zea mays L.). Strong stalks reduce lodging and maximize harvestable yield. Studies show rind penetrometer resistance (RPR), or the force required to pierce a stalk rind with a spike, is a valid approximation of strength. We measured RPR across 4,892 recombinant inbreds (RILs) comprising the maize nested association mapping (NAM) panel derived from crosses of diverse inbreds to the inbred, B73. An intermated B73 x Mo17 family (IBM) of 193 RILs and a panel of 2,453 diverse inbreds from the North Central Regional Plant Introduction Station (NCRPIS) were also evaluated. We measured RPR in three environments. Family-nested QTL were identified by joint-linkage mapping in the NAM panel. We also performed a genome-wide association study (GWAS) and genomic best linear unbiased prediction (GBLUP) in each panel. Broad sense heritability computed on a line means basis was low for RPR. Only 8 of 26 families had a heritability above 0.20. The NCRPIS diversity panel had a heritability of 0.54. Across the NAM and IBM families, 18 family-nested QTL and 141 significant GWAS associations were identified for RPR. Numerous weak associations were also found in the NCRPIS diversity panel. However, few were linked to loci involved in phenylpropanoid and cellulose synthesis or in vegetative phase transition. Using an identity-by-state (IBS) relationship matrix estimated from 1.6 million polymorphisms and RPR measures from 20% of the NAM panel, genomic prediction by GBLUP explained 64±2% of variation in the remaining RILs. In the NCRPIS diversity panel, an IBS matrix estimated from 681,257 polymorphisms and RPR measures from 20% of the panel explained 28±3% of variation in the remaining inbreds. These results indicate the high genetic complexity of stalk strength and the potential for genomic prediction to hasten its improvement.