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Genetic Basis of Yield and Yield Stability in Major Crops

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Crop Physiology and Crop Production".

Deadline for manuscript submissions: closed (20 February 2023) | Viewed by 41649

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Special Issue Editors

Prof. Dr. Wolfgang Friedt

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Guest Editor

Plant Breeding Department, Justus Liebig University, 35392 Giessen, Germany
Interests: plant biotechnology; plant genetics; plant breeding; plant genomics; molecular breeding; cereals; oil and protein crops; agronomy

Prof. Dr. Frank Ordon

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Guest Editor

Julius Kuehn-Institute, 06484 Quedlinburg, Germany
Interests: wheat and barley; molecular breeding; resistance to biotic and abiotic stress

Dr. Andreas Stahl

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Guest Editor

Julius Kuehn-Institute, 06484 Quedlinburg, Germany
Interests: nitrogen use efficiency (NUE); Plant Breeding; digital plant phenotyping; heterosis; genetic variation in root traits
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Dear Colleagues,

Feeding the earth´s growing population in the face of climate change while meeting Sustainable Development Goals is a major challenge for mankind. To achieve this, on the one hand yield increase is needed but also improvements in yield stability. All plant production starts with seeds, so plant breeding is of prime importance to meet these challenges, i.e., to increase yield and yield stability by improving resistance to biotic and abiotic stress.

To achieve this, a deeper understanding of the genetic determinants of yield-forming and yield-securing traits is indispensable. With the availability of genome sequencing data, new phenotyping approaches, and the advent of modern data analysis tools, breeding researchers can better understand genotype to phenotype relationships in different environments.

In this context, this Special Issue focuses on studies designed to contribute to our genetic knowledge of yield and yield stability in cereals, oil and protein crops, as well as root and tuber crops. This includes studies on abiotic and biotic stress factors and methodologically comprises the full spectrum of forward and reverse genetics, including state-of-the-art approaches of genomic prediction and genome editing.

Prof. Dr. Wolfgang Friedt
Prof. Dr. Frank Ordon
Dr. Andreas Stahl
Guest Editors

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Keywords

crop plants
cereals
oil and protein crops
root and tuber crops
yield-related traits
phenotyping
inheritance, heritability
molecular genetics
genotyping, marker-assisted selection
genomic prediction
ecological implications

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Published Papers (12 papers)

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Research

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14 pages, 4409 KiB

Open AccessArticle

Identification of Potential QTLs Related to Grain Size in Rice

by Jae-Ryoung Park, Jeonghwan Seo, Songhee Park, Mina Jin, O-Young Jeong and Hyun-Su Park

Plants 2023, 12(9), 1766; https://doi.org/10.3390/plants12091766 - 26 Apr 2023

Cited by 1 | Viewed by 1953

Abstract

Rice is a major crop, providing calories and food for most of the world’s population. Currently, the global population is rapidly increasing, and securing a yield of rice that can satisfy everyone is an ongoing challenge. The yield of rice can be increased by controlling 1000-grain weight as one of the important determining factors. Grain length, grain width, grain thickness, and 1000-grain weight, which determine grain size, are controlled by QTLs. To identify QTLs related to grain size, we screened and then mapped 88 RIL individuals derived from a cross between JJ625LG, which has a long grain size, long spindle-shaped grains, and low 1000-grain weight, and Namchan, which has short grains with round shape and heavy 1000-grain weight. In 2021 and 2022, 511 SNP markers were used to map QTLs related to grain size to a physical map. The QTLs found to be related to grain size are evenly distributed on chromosomes 2, 3, 5, 10, and 11. The mapping results also show that the QTLs qGl3-2, qRlw3, and qRlw3-2 of chromosome 3, and qGt5 and qRlw5 of chromosome 5 are, respectively, associated with GS3 and qSW5, which are the major genes previously cloned and found to be related to grain size. In addition, qGw10 and qGw10-1, which were additionally detected in this study, were found to be associated with Os10g0525200 (OsCPq10), a potential candidate gene involved in controlling grain size. This gene codes for a cytochrome P450 family protein and is reported to have a positive effect on grain size by interacting with proteins related to mechanisms determining grain size. In particular, OsCPq10 was screened in the same identified QTL region for 2 consecutive years, which is expected to have a positive effect on grain size. These results will be helpful for breeding elite rice cultivars with high yields through additional fine mapping related to grain size. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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16 pages, 3647 KiB

Open AccessArticle

Do We Need to Breed for Regional Adaptation in Soybean?—Evaluation of Genotype-by-Location Interaction and Trait Stability of Soybean in Germany

by Cleo A. Döttinger, Volker Hahn, Willmar L. Leiser and Tobias Würschum

Plants 2023, 12(4), 756; https://doi.org/10.3390/plants12040756 - 8 Feb 2023

Cited by 5 | Viewed by 2023

Abstract

Soybean is a crop in high demand, in particular as a crucial source of plant protein. As a short-day plant, soybean is sensitive to the latitude of the growing site. Consequently, varieties that are well adapted to higher latitudes are required to expand the cultivation. In this study, we employed 50 soybean genotypes to perform a multi-location trial at seven locations across Germany in 2021. Two environmental target regions were determined following the latitude of the locations. Adaptation and trait stability of seed yield and protein content across all locations were evaluated using Genotype plus Genotype-by-Environment (GGE) biplots and Shukla’s stability variance. We found a moderate level of crossing-over type genotype-by-location interaction across all locations. Within the environmental target regions, the genotype-by-location interaction could be minimised. Despite the positive correlation (R = 0.59) of seed yield between the environmental target regions and the same best-performing genotype, the genotype rankings differed in part substantially. In conclusion, we found that soybean can be grown at a wide range of latitudes across Germany. However, the performance of genotypes differed between the northern and southern locations, with an 18.8% higher mean yield in the south. This in combination with the observed rank changes of high-performing genotypes between both environmental target regions suggests that selection targeted towards environments in northern Germany could improve soybean breeding for those higher latitude regions. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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27 pages, 3479 KiB

Open AccessEditor’s ChoiceArticle

Optimal Contribution Selection Improves the Rate of Genetic Gain in Grain Yield and Yield Stability in Spring Canola in Australia and Canada

by Wallace A. Cowling, Felipe A. Castro-Urrea, Katia T. Stefanova, Li Li, Robert G. Banks, Renu Saradadevi, Olaf Sass, Brian P. Kinghorn and Kadambot H. M. Siddique

Plants 2023, 12(2), 383; https://doi.org/10.3390/plants12020383 - 13 Jan 2023

Cited by 11 | Viewed by 4976

Abstract

Crop breeding must achieve higher rates of genetic gain in grain yield (GY) and yield stability to meet future food demands in a changing climate. Optimal contributions selection (OCS) based on an index of key economic traits should increase the rate of genetic gain while minimising population inbreeding. Here we apply OCS in a global spring oilseed rape (canola) breeding program during three cycles of S_0,1 family selection in 2016, 2018, and 2020, with several field trials per cycle in Australia and Canada. Economic weights in the index promoted high GY, seed oil, protein in meal, and Phoma stem canker (blackleg) disease resistance while maintaining plant height, flowering time, oleic acid, and seed size and decreasing glucosinolate content. After factor analytic modelling of the genotype-by-environment interaction for the additive effects, the linear rate of genetic gain in GY across cycles was 0.059 or 0.087 t ha⁻¹ y⁻¹ (2.9% or 4.3% y⁻¹) based on genotype scores for the first factor (f₁) expressed in trait units or average predicted breeding values across environments, respectively. Both GY and yield stability, defined as the root-mean-square deviation from the regression line associated with f₁, were predicted to improve in the next cycle with a low achieved mean parental coancestry (0.087). These methods achieved rapid genetic gain in GY and other traits and are predicted to improve yield stability across global spring canola environments. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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18 pages, 2290 KiB

Open AccessArticle

Identification of Newer Stable Genetic Sources for High Grain Number per Panicle and Understanding the Gene Action for Important Panicle Traits in Rice

by Ariharasutharsan Gunasekaran, Geetha Seshadri, Saraswathi Ramasamy, Raveendran Muthurajan and Krishna Surendar Karuppasamy

Plants 2023, 12(2), 250; https://doi.org/10.3390/plants12020250 - 5 Jan 2023

Cited by 7 | Viewed by 2738

Abstract

Rice is an important food crop extensively cultivated worldwide, and rice’s grain yield should be improved to meet future food demand. Grain number per panicle is the main trait that determines the grain yield in rice, and other panicle-related traits influence the grain number. To study the genetic diversity, 50 diverse Indian-origin germplasm were evaluated for grain number per panicle and other panicle traits for two consecutive seasons (Rabi 2019 and Kharif 2020). The maximum genotypic and phenotypic coefficient of variation was obtained for the number of spikelets and filled grains per panicle. The genotypes were grouped into eight clusters with Mahalanobis’ D² analysis and six groups using Principal component analysis. Based on, per se, performance for grain number per panicle and genetic distances, six parents were selected and subjected to full diallel mating. The genotypes CB12132, IET 28749, and BPT 5204 were the best general combiners for the number of filled grains per panicle and other panicle branching traits, viz., the number of primary and secondary branches per panicle. The hybrid BPT 5204 × CB 12132 identified as the best specific combination for most of the studied panicle traits. The additive gene effects were high for the number of filled grains per panicle, the number of primary branches, and secondary branches, whereas non-additive gene action was high for the number of productive tillers and grain yield per plant. The information obtained from this study will be useful in rice breeding programs to improve panicle traits, especially the grain number, which would result in higher grain yield. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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26 pages, 12201 KiB

Open AccessArticle

Unraveling Genomic Regions Controlling Root Traits as a Function of Nitrogen Availability in the MAGIC Wheat Population WM-800

by Laura Schmidt, Kerstin A. Nagel, Anna Galinski, Wiebke Sannemann, Klaus Pillen and Andreas Maurer

Plants 2022, 11(24), 3520; https://doi.org/10.3390/plants11243520 - 14 Dec 2022

Cited by 3 | Viewed by 1888

Abstract

An ever-growing world population demands to be fed in the future and environmental protection and climate change need to be taken into account. An important factor here is nitrogen uptake efficiency (NUpE), which is influenced by the root system (the interface between plant and soil). To understand the natural variation of root system architecture (RSA) as a function of nitrogen (N) availability, a subset of the multiparent advanced generation intercross (MAGIC) winter wheat population WM-800 was phenotyped under two contrasting N treatments in a high-throughput phenotyping system at the seedling stage. Fourteen root and shoot traits were measured. Subsequently, these traits were genetically analyzed using 13,060 polymorphic haplotypes and SNPs in a genome-wide association study (GWAS). In total, 64 quantitative trait loci (QTL) were detected; 60 of them were N treatment specific. Candidate genes for the detected QTL included NRT1.1 and genes involved in stress signaling under N−, whereas candidate genes under N+ were more associated with general growth, such as mei2 and TaWOX11b. This finding may indicate (i) a disparity of the genetic control of root development under low and high N supply and, furthermore, (ii) the need for an N specific selection of genes and genotypes in breeding new wheat cultivars with improved NUpE. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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26 pages, 2243 KiB

Open AccessArticle

A Haplotype-Based GWAS Identified Trait-Improving QTL Alleles Controlling Agronomic Traits under Contrasting Nitrogen Fertilization Treatments in the MAGIC Wheat Population WM-800

by Antonia Lisker, Andreas Maurer, Thomas Schmutzer, Ebrahim Kazman, Hilmar Cöster, Josef Holzapfel, Erhard Ebmeyer, Ahmad M. Alqudah, Wiebke Sannemann and Klaus Pillen

Plants 2022, 11(24), 3508; https://doi.org/10.3390/plants11243508 - 14 Dec 2022

Cited by 6 | Viewed by 2213

Abstract

The multi-parent-advanced-generation-intercross (MAGIC) population WM-800 was developed by intercrossing eight modern winter wheat cultivars to enhance the genetic diversity present in breeding populations. We cultivated WM-800 during two seasons in seven environments under two contrasting nitrogen fertilization treatments. WM-800 lines exhibited highly significant differences between treatments, as well as high heritabilities among the seven agronomic traits studied. The highest-yielding WM-line achieved an average yield increase of 4.40 dt/ha (5.2%) compared to the best founder cultivar Tobak. The subsequent genome-wide-association-study (GWAS), which was based on haplotypes, located QTL for seven agronomic traits including grain yield. In total, 40, 51, and 46 QTL were detected under low, high, and across nitrogen treatments, respectively. For example, the effect of QYLD_3A could be associated with the haplotype allele of cultivar Julius increasing yield by an average of 4.47 dt/ha (5.2%). A novel QTL on chromosome 2B exhibited pleiotropic effects, acting simultaneously on three-grain yield components (ears-per-square-meter, grains-per-ear, and thousand-grain-weight) and plant-height. These effects may be explained by a member of the nitrate-transporter-1 (NRT1)/peptide-family, TaNPF5.34, located 1.05 Mb apart. The WM-800 lines and favorable QTL haplotypes, associated with yield improvements, are currently implemented in wheat breeding programs to develop advanced nitrogen-use efficient wheat cultivars. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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14 pages, 1415 KiB

Open AccessArticle

The Potential of Genome-Wide Prediction to Support Parental Selection, Evaluated with Data from a Commercial Barley Breeding Program

by Maximilian Rembe, Yusheng Zhao, Neele Wendler, Klaus Oldach, Viktor Korzun and Jochen C. Reif

Plants 2022, 11(19), 2564; https://doi.org/10.3390/plants11192564 - 29 Sep 2022

Cited by 3 | Viewed by 1781

Abstract

Parental selection is at the beginning and contributes significantly to the success of any breeding work. The value of a cross is reflected in the potential of its progeny population. Breeders invest substantial resources in evaluating progeny to select the best performing genotypes as candidates for variety development. Several proposals have been made to use genomics to support parental selection. These have mostly been evaluated using theoretical considerations or simulation studies. However, evaluations using experimental data have rarely been conducted. In this study, we tested the potential of genomic prediction for predicting the progeny mean, variance, and usefulness criterion using data from an applied breeding population for winter barley. For three traits with genetic architectures at varying levels of complexity, ear emergence, plant height, and grain yield, progeny mean, variance, and usefulness criterion were predicted and validated in scenarios resembling situations in which the described tools shall be used in plant breeding. While the population mean could be predicted with moderate to high prediction abilities amounting to 0.64, 0.21, and 0.39 in ear emergence, plant height, and grain yield, respectively, the prediction of family variance appeared difficult, as reflected in low prediction abilities of 0.41, 0.11, and 0.14, for ear emergence, plant height, and grain yield, respectively. We have shown that identifying superior crosses remains a challenging task and suggest that the success of predicting the usefulness criterion depends strongly on the complexity of the underlying trait. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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16 pages, 710 KiB

Open AccessArticle

Genetics of the Inverse Relationship between Grain Yield and Grain Protein Content in Common Wheat

by Manuel Geyer, Volker Mohler and Lorenz Hartl

Plants 2022, 11(16), 2146; https://doi.org/10.3390/plants11162146 - 18 Aug 2022

Cited by 17 | Viewed by 2450

Abstract

Grain protein content (GPC) is one of the most important criteria to determine the quality of common wheat (Triticum aestivum). One of the major obstacles for bread wheat production is the negative correlation between GPC and grain yield (GY). Previous studies demonstrated that the deviation from this inverse relationship is highly heritable. However, little is known about the genetics controlling these deviations in common wheat. To fill this gap, we performed quantitative trait locus (QTL) analysis for GY, GPC, and four derived GY-GPC indices using an eight-way multiparent advanced generation intercross population comprising 394 lines. Interval mapping was conducted using phenotypic data from up to nine environments and genotypic data from a 20k single-nucleotide polymorphism array. The four indices were highly heritable (0.76–0.88) and showed distinct correlations to GY and GPC. Interval mapping revealed that GY, GPC, and GY-GPC indices were controlled by 6, 12, and 12 unique QTL, of which each explained only a small amount of phenotypic variance (R² ≤ 10%). Ten of the 12 index QTL were independent of loci affecting GY and GPC. QTL regions harboured several candidate genes, including Rht-1, WAPO-A1, TaTEF-7A, and NRT2.6-7A. The study confirmed the usefulness of indices to mitigate the inverse GY-GPC relationship in breeding, though the selection method should reflect their polygenic inheritance. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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Review

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32 pages, 2466 KiB

Open AccessEditor’s ChoiceReview

The Past, Present, and Future of Wheat Dwarf Virus Management—A Review

by Anne-Kathrin Pfrieme, Torsten Will, Klaus Pillen and Andreas Stahl

Plants 2023, 12(20), 3633; https://doi.org/10.3390/plants12203633 - 20 Oct 2023

Cited by 3 | Viewed by 2652

Abstract

Wheat dwarf disease (WDD) is an important disease of monocotyledonous species, including economically important cereals. The causative pathogen, wheat dwarf virus (WDV), is persistently transmitted mainly by the leafhopper Psammotettix alienus and can lead to high yield losses. Due to climate change, the periods of vector activity increased, and the vectors have spread to new habitats, leading to an increased importance of WDV in large parts of Europe. In the light of integrated pest management, cultivation practices and the use of resistant/tolerant host plants are currently the only effective methods to control WDV. However, knowledge of the pathosystem and epidemiology of WDD is limited, and the few known sources of genetic tolerance indicate that further research is needed. Considering the economic importance of WDD and its likely increasing relevance in the coming decades, this study provides a comprehensive compilation of knowledge on the most important aspects with information on the causal virus, its vector, symptoms, host range, and control strategies. In addition, the current status of genetic and breeding efforts to control and manage this disease in wheat will be discussed, as this is crucial to effectively manage the disease under changing environmental conditions and minimize impending yield losses. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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16 pages, 1370 KiB

Open AccessReview

The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics

by Jaco D. Zandberg, Cassandria T. Fernandez, Monica F. Danilevicz, William J. W. Thomas, David Edwards and Jacqueline Batley

Plants 2022, 11(20), 2740; https://doi.org/10.3390/plants11202740 - 17 Oct 2022

Cited by 8 | Viewed by 4306

Abstract

The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by >450 fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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27 pages, 6550 KiB

Open AccessReview

Improving Yield and Yield Stability in Winter Rye by Hybrid Breeding

by Bernd Hackauf, Dörthe Siekmann and Franz Joachim Fromme

Plants 2022, 11(19), 2666; https://doi.org/10.3390/plants11192666 - 10 Oct 2022

Cited by 19 | Viewed by 11495

Abstract

Rye is the only cross-pollinating small-grain cereal. The unique reproduction biology results in an exceptional complexity concerning genetic improvement of rye by breeding. Rye is a close relative of wheat and has a strong adaptation potential that refers to its mating system, making this overlooked cereal readily adjustable to a changing environment. Rye breeding addresses the emerging challenges of food security associated with climate change. The systematic identification, management, and use of its valuable natural diversity became a feasible option in outbreeding rye only following the establishment of hybrid breeding late in the 20th century. In this article, we review the most recent technological advances to improve yield and yield stability in winter rye. Based on recently released reference genome sequences, SMART breeding approaches are described to counterbalance undesired linkage drag effects of major restorer genes on grain yield. We present the development of gibberellin-sensitive semidwarf hybrids as a novel plant breeding innovation based on an approach that is different from current methods of increasing productivity in rye and wheat. Breeding of new rye cultivars with improved performance and resilience is indispensable for a renaissance of this healthy minor cereal as a homogeneous commodity with cultural relevance in Europe that allows for comparatively smooth but substantial complementation of wheat with rye-based diets, supporting the necessary restoration of the balance between human action and nature. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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Other

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13 pages, 2642 KiB

Open AccessCase Report

Genetic Analysis for the Flag Leaf Heterosis of a Super-Hybrid Rice WFYT025 Combination Using RNA-Seq

by Qin Cheng, Shiying Huang, Lan Lin, Qi Zhong, Tao Huang, Haohua He and Jianmin Bian

Plants 2023, 12(13), 2496; https://doi.org/10.3390/plants12132496 - 29 Jun 2023

Cited by 1 | Viewed by 1532

Abstract

The photosynthetic capacity of flag leaf plays a key role in grain yield in rice. Nevertheless, there are few studies on the heterosis of the rice flag leaf. Therefore, this study focuses on investigating the genetic basis of heterosis for flag leaf in the indica super hybrid rice combination WFYT025 in China using a high-throughput next-generation RNA-seq strategy. We analyzed the gene expression of flag leaf in different environments and different time periods between WFYT025 and its female parent. After obtaining the gene expression profile of the flag leaf, we further investigated the gene regulatory network. Weighted gene expression network analysis (WGCNA) was used to identify the co-expressed gene sets, and a total of 5000 highly expressed genes were divided into 24 co-expression groups. In CHT025, we found 13 WRKY family transcription factors in SDG_hps under the environment of early rice and 16 WRKY family genes in SDG_hps of under the environment of middle rice. We found nine identical transcription factors in the two stages. Except for five reported TFs, the other four TFs might play an important role in heterosis for grain number and photosynthesis. Transcription factors such as WRKY3, WRKY68, and WRKY77 were found in both environments. To eliminate the influence of the environment, we examined the metabolic pathway with the same SDG_hp (SSDG_hp) in two environments. There were 312 SSDG_hps in total. These SSDG_hps mainly focused on the phosphorus metallic process, phosphorylation, plasma membrane, etc. These results provide resources for studying heterosis during super hybrid rice flag leaf development. Full article

(This article belongs to the Special Issue Genetic Basis of Yield and Yield Stability in Major Crops)

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