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1. Convergent selection of a WD40 protein that enhances grain yield in maize and rice

   https://doi.org/10.1126/science.abg7985  

   Chen, Wenkang ; Chen, Lu ; Zhang, Xuan ; Yang, Ning ; Guo, Jianghua ; Wang, Min ; Ji, Shenghui ; Zhao, Xiangyu ; Yin, Pengfei ; Cai, Lichun ; et al ( March 2022 , Science)

   INTRODUCTION During the independent process of cereal evolution, many trait shifts appear to have been under convergent selection to meet the specific needs of humans. Identification of convergently selected genes across cereals could help to clarify the evolution of crop species and to accelerate breeding programs. In the past several decades, researchers have debated whether convergent phenotypic selection in distinct lineages is driven by conserved molecular changes or by diverse molecular pathways. Two of the most economically important crops, maize and rice, display some conserved phenotypic shifts—including loss of seed dispersal, decreased seed dormancy, and increased grain number during evolution—even though they experienced independent selection. Hence, maize and rice can serve as an excellent system for understanding the extent of convergent selection among cereals. RATIONALE Despite the identification of a few convergently selected genes, our understanding of the extent of molecular convergence on a genome-wide scale between maize and rice is very limited. To learn how often selection acts on orthologous genes, we investigated the functions and molecular evolution of the grain yield quantitative trait locus KRN2 in maize and its rice ortholog OsKRN2 . We also identified convergently selected genes on a genome-wide scale in maize and rice, using two large datasets. RESULTS We identified a selected gene, KRN2 ( kernel row number2 ), that differs between domesticated maize and its wild ancestor, teosinte. This gene underlies a major quantitative trait locus for kernel row number in maize. Selection in the noncoding upstream regions resulted in a reduction of KRN2 expression and an increased grain number through an increase in kernel rows. The rice ortholog, OsKRN2 , also underwent selection and negatively regulates grain number via control of secondary panicle branches. These orthologs encode WD40 proteins and function synergistically with a gene of unknown function, DUF1644, which suggests that a conserved protein interaction controls grain number in maize and rice. Field tests show that knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by ~10% and ~8%, respectively, with no apparent trade-off in other agronomic traits. This suggests potential applications of KRN2 and its orthologs for crop improvement. On a genome-wide scale, we identified a set of 490 orthologous genes that underwent convergent selection during maize and rice evolution, including KRN2/OsKRN2 . We found that the convergently selected orthologous genes appear to be significantly enriched in two specific pathways in both maize and rice: starch and sucrose metabolism, and biosynthesis of cofactors. A deep analysis of convergently selected genes in the starch metabolic pathway indicates that the degree of genetic convergence via convergent selection is related to the conservation and complexity of the gene network for a given selection. CONCLUSION Our findings show that common phenotypic shifts during maize and rice evolution acting on conserved genes are driven at least in part by convergent selection, which in maize and rice likely occurred both during and after domestication. We provide evolutionary and functional evidence on the convergent selection of KRN2/OsKRN2 for grain number between maize and rice. We further found that a complete loss-of-function allele of KRN2/OsKRN2 increased grain yield without an apparent negative impact on other agronomic traits. Exploring the role of KRN2/OsKRN2 and other convergently selected genes across the cereals could provide new opportunities to enhance the production of other global crops. Shared selected orthologous genes in maize and rice for convergent phenotypic shifts during domestication and improvement. By comparing 3163 selected genes in maize and 18,755 selected genes in rice, we identified 490 orthologous gene pairs, including KRN2 and its rice ortholog OsKRN2 , as having been convergently selected. Knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by increasing kernel rows and secondary panicle branches, respectively. 

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2. Breeding crops for drought-affected environments and improved climate resilience

   https://doi.org/10.1093/plcell/koac321  

   Cooper, Mark ; Messina, Carlos D. ( November 2022 , The Plant Cell)

   Breeding climate-resilient crops with improved levels of abiotic and biotic stress resistance as a response to climate change presents both opportunities and challenges. Applying the framework of the “breeder’s equation,” which is used to predict the response to selection for a breeding program cycle, we review methodologies and strategies that have been used to successfully breed crops with improved levels of drought resistance, where the target population of environments (TPEs) is a spatially and temporally heterogeneous mixture of drought-affected and favorable (water-sufficient) environments. Long-term improvement of temperate maize for the US corn belt is used as a case study and compared with progress for other crops and geographies. Integration of trait information across scales, from genomes to ecosystems, is needed to accurately predict yield outcomes for genotypes within the current and future TPEs. This will require transdisciplinary teams to explore, identify, and exploit novel opportunities to accelerate breeding program outcomes; both improved germplasm resources and improved products (cultivars, hybrids, clones, and populations) that outperform and replace the products in use by farmers, in combination with modified agronomic management strategies suited to their local environments.

    

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3. The combined and separate impacts of climate extremes on the current and future US rainfed maize and soybean production under elevated CO 2

   https://doi.org/10.1111/gcb.13617  

   Jin, Zhenong ; Zhuang, Qianlai ; Wang, Jiali ; Archontoulis, Sotirios V. ; Zobel, Zachary ; Kotamarthi, Veerabhadra R. ( January 2017 , Global Change Biology)

   Heat and drought are two emerging climatic threats to theUSmaize and soybean production, yet their impacts on yields are collectively determined by the magnitude of climate change and rising atmosphericCO₂concentrations. This study quantifies the combined and separate impacts of high temperature, heat and drought stresses on the current and futureUSrainfed maize and soybean production and for the first time characterizes spatial shifts in the relative importance of individual stress. Crop yields are simulated using the Agricultural Production Systems Simulator (APSIM), driven by high‐resolution (12 km) dynamically downscaled climate projections for 1995–2004 and 2085–2094. Results show that maize and soybean yield losses are prominent in theUSMidwest by the late 21st century under both Representative Concentration Pathway (RCP) 4.5 andRCP8.5 scenarios, and the magnitude of loss highly depends on the current vulnerability and changes in climate extremes. Elevated atmosphericCO₂partially but not completely offsets the yield gaps caused by climate extremes, and the effect is greater in soybean than in maize. Our simulations suggest that drought will continue to be the largest threat toUSrainfed maize production underRCP4.5 and soybean production under bothRCPscenarios, whereas high temperature and heat stress take over the dominant stress of drought on maize underRCP8.5. We also reveal that shifts in the geographic distributions of dominant stresses are characterized by the increase in concurrent stresses, especially for theUSMidwest. These findings imply the importance of considering heat and drought stresses simultaneously for future agronomic adaptation and mitigation strategies, particularly for breeding programs and crop management. The modeling framework of partitioning the total effects of climate change into individual stress impacts can be applied to the study of other crops and agriculture systems.

    

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4. Predictive breeding for maize: Making use of molecular phenotypes, machine learning, and physiological crop models

   https://doi.org/10.1002/csc2.20052  

   Washburn, Jacob D. ; Burch, Merritt B. ; Franco, José A. ( March 2020 , Crop Science)

   Maize (Zea mays L.) has been a focus of scientific research and breeding for over a century. It is also one of the most economically important crops in the world, with a value of approximately US$50 billion per year in the United States alone. Additionally, maize has long been the model species of choice for the study and exploitation of hybrid vigor, and it continues to be one of the world's most efficient converters of photosynthetic energy into starch. This review discusses the history and future of maize predictive breeding in the context of both genotype centric methods, and those focusing on genotype × environment × management interactions. Current prediction challenges are highlighted, as well as important advances in technology, methods, datasets, interdisciplinary collaborations, and scientific culture that will enable accelerated progress in predictive maize (and other crop species) breeding for years to come. 

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5. The important but weakening maize yield benefit of grain filling prolongation in the US Midwest

   https://doi.org/10.1111/gcb.14356  

   Zhu, Peng ; Jin, Zhenong ; Zhuang, Qianlai ; Ciais, Philippe ; Bernacchi, Carl ; Wang, Xuhui ; Makowski, David ; Lobell, David ( July 2018 , Global Change Biology)

   A better understanding of recent crop yield trends is necessary for improving the yield and maintaining food security. Several possible mechanisms have been investigated recently in order to explain the steady growth in maize yield over theUSCorn‐Belt, but a substantial fraction of the increasing trend remains elusive. In this study, trends in grain filling period (GFP) were identified and their relations with maize yield increase were further analyzed. Using satellite data from 2000 to 2015, an average lengthening ofGFPof 0.37 days per year was found over the region, which probably results from variety renewal. Statistical analysis suggests that longerGFPaccounted for roughly one‐quarter (23%) of the yield increase trend by promoting kernel dry matter accumulation, yet had less yield benefit in hotter counties. Both official survey data and crop model simulations estimated a similar contribution ofGFPtrend to yield. If growing degree days that determines theGFPcontinues to prolong at the current rate for the next 50 years, yield reduction will be lessened with 25% and 18% longerGFPunder Representative Concentration Pathway 2.6 (RCP2.6) andRCP6.0, respectively. However, this level of progress is insufficient to offset yield losses in future climates, because drought and heat stress during theGFPwill become more prevalent and severe. This study highlights the need to devise multiple effective adaptation strategies to withstand the upcoming challenges in food security.

    

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