Maize Genetics Cooperation Newsletter vol 87 2013

Quantitative Trait Loci for Leaf Angle, Leaf Width, Leaf Length, and Plant Height in IBM-94

James Wassom, unaffiliated, Sioux Falls, SD

[email protected]

Introduction

Modern maize varieties are more productive than varieties of a few decades ago, partly due to higher population densities and adaptations that permit vigorous growth at high densities. Plant forms that enable efficient light interception at high population densities will increase yield production under modern field conditions. Leaf angle has been shown to affect yield especially at high densities. To determine the QTL affecting leaf traits and plant height in maize I experimented with IBM-94, a B73 x Mo17 recombinant inbred line (RIL) population developed by other researchers for genetic studies (Lee et al 2002, Coe et al 2002, Cone et al 2002).

Materials and Methods

Seed for the 93 RIL constituting IBM-94 was obtained from the Maize Genetics Cooperative Stock Center (http://maizecoop.cropsci.uiuc.edu). In year 2006 the original seed was grown and plants were self-pollinated to produce enough RIL seed to plant replicated experimental plots at Sioux Falls, SD, USA. In years 2007, 2008, and 2009 the 93 RIL were grown in randomized complete blocks with three replicates each year. Space was limited, so each plot included four plants spaced 279 mm apart in rows 76 mm apart. There were no extra spaces between plots in rows. At anthesis or soon after, the total plant height to the tassle tip and the leaf at the uppermost ear shoot were measured on the two center plants in each plot. Leaf measurements included the leaf angle from vertical, maximum leaf width, and distance from the ligule to the tip of the straightened leaf.

Statistical analysis, including analysis of variance and heritability was performed with PLABSTAT (University of Hohenheim, Germany, https://plant-breeding.uni-hohenheim.de/~ipspwww/soft.html). Genetic map distances of markers and molecular marker genotypes of each RIL was obtained from the Maize Genetics and Genomics Database (MaizeGDB) (http://www.maizegdb.org). Phenotype data for the RILs was combined with marker genotypic information and map distances from the MaizeGDB IBM2 map to analyze for QTL using PLABMQTL (University of Hohenheim, Germany, https://plant-breeding.uni-hohenheim.de/~ipspwww/soft.html).

Results

There was significant variation among genotypes (Table 1) and 1 to 3 QTL identified for each of the measured traits (Table 2). Larger plots and the larger IBM-302 population might have improved precision and enabled detection of more QTL. The total area taken up by nursery rows and experimental plots was about 50 by 75 feet, illustrating that even with limited resources the IBM-94 population and MaizeGDB data can be used for QTL mapping.

References

Coe E, Cone K, McMullen M, Chen SS, Davis G, Gardiner J, Liscum E, Polacco ML, Paterson A, Sanchez-Villeda H, Soderlumd C, Wing R. 2002. Access to the maize genome: An integrated physical and genetic map. Plant Physiol 128: 9-12

Cone KC, McMullen MD, Bi IV, Davis GL, Yim Y-S, Gardiner JS, Polacco ML, Sanchez-Villeda H, Fang Z, Schroeder SG, Havermann SA, Bowers JE, Paterson AH, Soderlumd CA, Engler FW, Wing RA, Coe EH Jr. 2002. Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol 130:1598-1605

Lee M., Sharapova N, Beavis WD, Grant D, Katt M, Blair D, and Hallauer A. 2002. Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol Biol 48:453-461

Table 1. Characterization of IBM-94 RIL grown at Sioux Falls, SD in 2007, 2008, and 2009.

	Leaf Angle		Leaf Width		Leaf Length		Plant Height
	Degrees		──────────────── mm ────────────────
RIL Mean ^�	26 � 2.6		91.0 � 2.95		764.6 � 20.76		2231.3 � 101.24
Range among RILs ^�	9 to 53		71.2 to 114.5		641.7 to 907.0		1323.2 to 2796.8
	ANOVA
Source of Variation	──────────────── MS, F ────────────────
Genotypes	623.8	10.49**	576.6	7.24**	26374	6.80**	362149	3.93**
Years	1026.0	9.54*	990.6	3.31	582080	35.41**	18780568	71.16**
Genotype × Year	59.5	1.68**	79.6	1.52**	3878	1.86**	92242	4.27**
Replications in Years	107.5	3.04**	299.2	5.72**	16436	7.87**	263924	12.21**
Error	35.3		52.3		2089		21617
	Variance Components and H^2
σ^2g	62.7 � 10.13		55.2 � 9.40		2500 � 429.8		29990 � 5965.4
σ^2e	3.3 � 2.61		2.5 � 2.57		2027 � 1475.5		66368 � 47600.4
σ^2ge	8.1 � 2.19		9.1 � 2.96		596 � 141.2		23542 � 3226.4
σ^2rep(^e)	0.8 � 0.58		2.7 � 1.61		154 � 88.4		2605 � 1419.0
σ ^2error	35.3 � 2.14		52.3 � 3.16		2089 � 126.2		1617 � 1304.8
H^2, %	90.47		86.20		85.30		74.53
H^2, 90% confidence int.	86.24, 93.26		80.08, 90.23		78.78, 89.59		63.25, 81.97

*,** Significant at α = 0.05, 0.01, respectively

^� � Standard error

Table 2. Regression models with QTL for leaf angle, leaf width, leaf length, and plant height in IBM94 RILs. The QTL were detected and included in regression models if LOD values in scans were greater than the LOD threshold corresponding to � = 0.05, by permutation test. Effects that are positive in sign are favored by the Mo17 allele.

Bin^�	Marker interval	Chrom. and position	CV^�	Support Interval^�	LOD	Partial R^2	Effect^�	R^2adj^#	�p ^��
Leaf Angle
1.05–1.05	umc1603–uaz273	1/480	59.8%	465–495	4.27	16.4%	-3.802	27.1%	32.5%
5.04–5.05	csu308–umc1482	5/375	44.6	345–390	4.80	13.9	3.084
9.01–9.01	umc1867–lim343	9/30	62.9	15–45	4.76	10.4	-2.760
Leaf Width
2.04–2.04	umc2088–umc2250	2/320	86.5	300–340	5.20	21.6	4.076	25.0	31.2
8.03–8.03	umc1735–php20714	8/280	85.9	260–300	5.28	15.2	-3.080
Leaf Length
2.09–2.09	bnlg1893–AY110389	2/660	54.4	640–680	4.08	11.1	-21.531	9.1	11.9
Plant Height
4.06–4.06	umc2027–AY110310	4/350	40.3	330–360	4.01	10.4	-26.64	8.4	32.1

*, ** α = 0.05 or 0.01, respectively, for the probability that this QTL affected the trait independently of other QTL.

^� Bins where the flanking markers are located and positions are the coordinate values on the MaizeGDB IBM2 map (http://www.maizegdb.org).

^� Frequency of detection within a 1-LOD support interval in 1000 CV runs with families randomly divided for detection and validation.

^� Interval with LOD scores within 1 LOD of the QTL peak

^� Effects were determined in a simultaneous multiple regression that included factors with LODs � the α = 0.05 threshold.

^# R² adjusted for the number of terms in the multiple regression models.

^�� The proportion of genotypic variance explained by all QTL in the models.

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of authors.