Author: Gary Atlin

Identification of QTL for early vigor and Stay-Green conferring tolerance to drought in two connected advanced backcross populations in Tropical Maize (Zea mays L.)

Gary Atlin Raman Babu XUECAI ZHANG (2016)

We aimed to identify quantitative trait loci (QTL) for secondary traits related to grain yield (GY) in two BC1F2:3 backcross populations (LPSpop and DTPpop) under well-watered (4 environments; WW) and drought stressed (6; DS) conditions to facilitate breeding efforts towards drought tolerant maize. GY reached 5.6 and 5.8 t/ha under WW in the LPSpop and the DTPpop, respectively. Under DS, grain yield was reduced by 65% (LPSpop) to 59% (DTPpop) relative to WW. GY was strongly associated with the normalized vegetative index (NDVI; r ranging from 0.61 to 0.96) across environmental conditions and with an early flowering under drought stressed conditions (r ranging from -0.18 to -0.25) indicative of the importance of early vigor and drought escape for GY. Out of the 105 detected QTL, 53 were overdominant indicative of strong heterosis. For 14 out of 18 detected vigor QTL, as well as for eight flowering time QTL the trait increasing allele was derived from CML491. Collocations of early vigor QTL with QTL for stay green (bin 2.02, WW, LPSpop; 2.07, DS, DTPpop), the number of ears per plant (bins 2.02, 2.05, WW, LPSpop; 5.02, DS, LPSpop) and GY (bin 2.07, WW, DTPpop; 5.04, WW, LPSpop), reinforce the importance of the observed correlations. LOD scores for early vigor QTL in these bins ranged from 2.2 to 11.25 explaining 4.6 (additivity: +0.28) to 19.9% (additivity: +0.49) of the observed phenotypic variance. A strong flowering QTL was detected in bin 2.06 across populations and environmental conditions explaining 26–31.3% of the observed phenotypic variation (LOD: 13–17; additivity: 0.1–0.6d). Improving drought tolerance while at the same time maintaining yield potential could be achieved by combining alleles conferring early vigor from the recurrent parent with alleles advancing flowering from the donor. Additionally bin 8.06 (DTPpop) harbored a QTL for GY under WW (additivity: 0.27 t/ha) and DS (additivity: 0.58 t/ha). R2 ranged from 0 (DTPpop, WW) to 26.54% (LPSpop, DS) for NDVI, 18.6 (LPSpop, WW) to 42.45% (LPSpop, DS) for anthesis and from 0 (DTPpop, DS) to 24.83% (LPSpop, WW) for GY. Lines out-yielding the best check by 32.5% (DTPpop, WW) to 60% (DTPpop, DS) for all population-by-irrigation treatment combination (except LPSpop, WW) identified are immediately available for the use by breeders.


Quantitative Trait Loci Drought resistance Zea mays CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

Rapid breeding and varietal replacement are critical to adaptation of cropping systems in the developing world to climate change

Gary Atlin Jill Cairns Biswanath Das (2017)

Plant breeding is a key mechanism for adaptation of cropping systems to climate change. Much discussion of breeding for climate change focuses on genes with large effects on heat and drought tolerance, but phenology and stress tolerance are highly polygenic. Adaptation will therefore mainly result from continually adjusting allele frequencies at many loci through rapid-cycle breeding that delivers a steady stream of incrementally improved cultivars. This will require access to elite germplasm from other regions, shortened breeding cycles, and multi-location testing systems that adequately sample the target population of environments. The objective of breeding and seed systems serving smallholder farmers should be to ensure that they use varieties developed in the last 10 years. Rapid varietal turnover must be supported by active dissemination of new varieties, and active withdrawal of obsolete ones. Commercial seed systems in temperate regions achieve this through competitive seed markets, but in the developing world, most crops are not served by competitive commercial seed systems, and many varieties date from the end of the Green Revolution (the late 1970s, when the second generation of modern rice and wheat varieties had been widely adopted). These obsolete varieties were developed in a climate different than today's, placing farmers at risk. To reduce this risk, a strengthened breeding system is needed, with freer international exchange of elite varieties, short breeding cycles, high selection intensity, wide-scale phenotyping, and accurate selection supported by genomic technology. Governments need to incentivize varietal release and dissemination systems to continuously replace obsolete varieties.


Cropping systems Climate change Plant breeding CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

META: A suite of sas programs to analyze multienvironment breeding trials

Mateo Vargas Hernández Gregorio Alvarado Gary Atlin Ky Mathews Jose Crossa (2013)

Multi-environment trials (METs) enable the evaluation of the same genotypes in a variety of environments and management conditions. We present here META (Multi Environment Trial Analysis), a suite of 31 SAS programs that analyze METs with complete or incomplete block designs, with or without adjustment by a covariate. The entire program is run through a graphical user interface. The program can produce boxplots or histograms for all traits, as well as univariate statistics. It also calculates Best Linear Unbiased Estimators (BLUEs) and Best Linear Unbiased Predictors (BLUPs) for the main response variable and BLUEs for all other traits. For all traits it calculates variance components by Restricted Maximum Likelihood (REML), Least Significant Differences (LSD), Coefficient of Variation (CV), and broad-sense heritability using PROC MIXED. The program can analyze each location separately, combine the analysis by management conditions, or combine all locations. The flexibility and simplicity of use of this program makes it a valuable tool for the analysis of METs in breeding and agronomy. The META program can be used by researcher knowing few principles of SAS.



Identification of donors for low-nitrogen stress with maize lethal necrosis (MLN) tolerance for maize breeding in sub-Saharan Africa

Biswanath Das Gary Atlin Michael Olsen Juan Burgueño Amsal Tarekegne Raman Babu rumbidzai matemba-mutasa Mainassara Zaman-Allah Prasanna Boddupalli Jill Cairns (2019)

After drought, a major challenge to smallholder farmers in sub-Saharan Africa is low-fertility soils with poor nitrogen (N)-supplying capacity. Many challenges in this region need to be overcome to create a viable fertilizer market. An intermediate solution is the development of maize varieties with an enhanced ability to take up or utilize N in severely depleted soils, and to more efficiently use the small amounts of N that farmers can supply to their crops. Over 400 elite inbred lines from seven maize breeding programs were screened to identify new sources of tolerance to low-N stress and maize lethal necrosis (MLN) for introgression into Africa-adapted elite germplasm. Lines with high levels of tolerance to both stresses were identified. Lines previously considered to be tolerant to low-N stress ranked in the bottom 10% under low-N confirming the need to replace these lines with new donors identified in this study. The lines that performed best under low-N yielded about 0. 5 Mg ha−1 (20%) more in testcross combinations than some widely used commercial parent lines such as CML442 and CML395. This is the first large scale study to identify maize inbred lines with tolerance to low-N stress and MLN in eastern and southern Africa.



Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments

Gary Atlin John Hickey Jose Crossa Jean-Luc Jannink Mark Sorrells Raman Babu Jill Cairns Amsal Tarekegne Kassa Semagn Yoseph Beyene Albrecht E. Melchinger (2012)

Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F2-derived lines from each of five populations. Although up to 25% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F2-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set.



Gains in maize genetic improvement in Eastern and Southern Africa: II. CIMMYT open-pollinated variety breeding pipeline

Benhildah Masuka Cosmos Magorokosho Michael Olsen Gary Atlin Marianne Bänziger Kevin Pixley Bindiganavile Vivek Maryke Labuschagne rumbidzai matemba-mutasa Juan Burgueño Prasanna Boddupalli Biswanath Das Dan Makumbi Amsal Tarekegne Jose Crossa Mainassara Zaman-Allah Jill Cairns (2017)

Open-pollinated varieties (OP Vs) still represent a significant proportion of the maize (Zea mays L.) seed system in many countries of sub- Saharan Africa. The International Maize and Wheat Improvement Centre (CIMMYT) has been breeding improved maize varieties for the stress-prone environments experienced by most smallholder farmers in eastern and southern Africa for over 30 yr. Hybrid breeding is now the major focus of the CIMMYT breeding pipeline. However, OP Vs are generated within the hybrid pipeline. This is the first study to document genetic gain for maize grain yield under both optimal and stress (random and managed drought, low nitrogen [N], and maize streak virus [MSV]) conditions within the CIMMYT eastern and southern African OP V breeding pipeline. Genetic gain was estimated using the slope of the regression on the year of OP V release in regional trials over a 12-yr period (1999–2011). Open-pollinated varieties were separated into two maturity groups, early (<70 d to anthesis) and intermediate-late (>70 d to anthesis). Genetic gain in the early maturity group under optimal conditions, random drought, low N, and MSV was 109.9, 29.2, 84.8, and 192.9 kg ha−1 yr−1. In the intermediate-late maturity group, genetic gain under optimal conditions, random drought, low N, and MSV was 79.1, 42.3, 53.0 and 108.7 kg ha−1 yr−1. No significant yield gains were made under managed drought stress for both maturity groups. Our results show continued improvement in OP Vs for both yield potential and stress tolerance.



Gains in maize genetic improvement in Eastern and Southern Africa: I. CIMMYT hybrid breeding pipeline

Benhildah Masuka Gary Atlin Michael Olsen Cosmos Magorokosho Maryke Labuschagne Jose Crossa Marianne Bänziger Kevin Pixley Bindiganavile Vivek Gregorio Alvarado Prasanna Boddupalli Dan Makumbi Amsal Tarekegne Biswanath Das Mainassara Zaman-Allah Jill Cairns (2017)

Monitoring of genetic gain in crop genetic improvement programs is necessary to measure the efficiency of the program. Periodic measurement of genetic gain also allows the efficiency of new technologies incorporated into a program to be quantified. Genetic gain within the International Maize and Wheat Improvement Centre (CIMMYT) breeding program for eastern and southern Africa were estimated using time series of maize (Zea mays L.) hybrids. A total of 67 of the best-performing hybrids from regional trials from 2000 to 2010 were selected to form an era panel and evaluated in 32 trials in eight locations across six countries in eastern and southern Africa. Treatments included optimal management, managed and random drought stress, low-nitrogen (N) stress and maize streak virus (MSV) infestation. Genetic gain was estimated as the slope of the regression of grain yield on the year of hybrid release. Genetic gain under optimal conditions, managed drought, random drought, low N, and MSV were estimated to have increased by 109.4, 32.5, 22.7, 20.9 and 141.3 kg ha−1 yr−1, respectively. These results are comparable with genetic gain in maize yields in other regions of the world. New technologies to further increase the rate of genetic gain in maize breeding for eastern and southern Africa are also discussed.