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Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance

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A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 14393

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Special Issue Editors

Dr. Jianlong Xu

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Guest Editor

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: QTL mapping; favorable allele mining; designed QTL pyramiding (DQP); molecular rice breeding; disease resistance; salt tolerance; drought tolerance

Prof. Dr. Meixue Zhou

E-Mail Website
Guest Editor

Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
Interests: cereal breeding; plant molecular biology; plant physiology
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Special Issue Information

Dear Colleagues,

With the global population increase, we are facing great challenges in the provision of sufficient grains to feed the world due to a decrease in arable land, inadequate water resources, and frequent natural disasters. Climatic changes lead to rising temperatures, more frequent floods, more diseases and pest outbreaks, and frequent abiotic stresses such as drought, saline, and alkaline stresses. Crop production under biotic and abiotic stresses is becoming increasingly vulnerable and unsustainable. In addressing these challenges within a global warming environment and ensuring food security, crop breeding has assumed paramount significance. In recent years, significant advances have been made in identifying favorable alleles for yield and its components, as well as tolerance to biotic and abiotic stresses. This has been accomplished through advanced genetic methodologies, encompassing reverse genetics, forward genetics (including genetic linkage mapping and genome-wide association mapping), and high-throughput phenotyping platforms. These achievements provide a robust foundation for transferring or pyramiding a series of favorable allelic variations that are usually dispersed in different genetic resources via genomic selection and other state-of-the-art breeding technologies such as precise genome editing and gene transformation.

Hence, the main aim of the proposed Special Issue is to gather research methods, innovations, and knowledge in the areas of mining and utilization of favorable alleles for yield and its components, and biotic and abiotic stress tolerance in crops.

We invite researchers to contribute their original research papers and reviews on the following themes. Potential topics include, but are not limited to, the following:

Candidate gene and favorable allele identification for yield, biotic and abiotic stress tolerance;
Favorable haplotype-based molecular breeding;
Genome editing for yield and stress tolerance improvement;
Introgressing and pyramiding favorable genes via genomic selection.

Dr. Jianlong Xu
Prof. Dr. Meixue Zhou
Guest Editors

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Keywords

high yield
biotic and abiotic stress tolerance
favorable gene editing
favorable gene transformation
genomic selection
favorable allele or haplotype identification
pyramiding breeding by molecular technology

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Published Papers (9 papers)

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Research

Jump to: Review

19 pages, 3360 KiB

Open AccessArticle

CRISPR/Cas9-Mediated Development of Potato Varieties with Long-Term Cold Storage and Bruising Resistance

by Gabriela Alejandra Massa, Cecilia Andrea Décima Oneto, Matías Nicolás González, Anabela Poulsen Hornum, Ailín Arizmendi, Sofía Sucar, Silvina Beatriz Divito and Sergio Enrique Feingold

Biology 2025, 14(4), 445; https://doi.org/10.3390/biology14040445 - 20 Apr 2025

Viewed by 341

Abstract

Enzymatic browning and cold-induced sweetening (CIS) affect the post-harvest quality of potato tubers. Browning is caused by polyphenol oxidase 2 (PPO2), which is activated by mechanical damage during harvest and storage. CIS occurs when vacuolar invertase converts sucrose into reducing sugars, which react with amino acids during frying, forming brown pigments and acrylamide. While cold storage prevents sprouting and disease, it also increases vacuolar invertase expression, leading to quality loss. Using CRISPR/Cas9, we developed gene-edited potato lines with improved resistance to browning and CIS. Line 6A (cv. Atlantic) and E03-3 (cv. Spunta) exhibited complete vacuolar invertase (InvVac) knockout, maintaining chip quality for at least 60 days at 4 °C. Line 6A, renamed PIRU INTA, was tested in field trials and preserved frying quality for up to 90 days under cold storage. PIRU INTA is currently undergoing registration as a new variety. Additionally, lines E04-5B and E03-3 (cv. Spunta) showed partial PPO2 gene edits, reducing enzymatic browning by 80% and 40%, respectively. This study demonstrates the potential of CRISPR/Cas9 to develop non-transgenic, gene-edited potatoes with enhanced storage quality, benefiting both growers and the food industry. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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23 pages, 4985 KiB

Open AccessArticle

Genome-Wide Dissection of Novel QTLs and Genes Associated with Weed Competitiveness in Early-Backcross Selective Introgression-Breeding Populations of Rice (Oryza sativa L.)

by Kim Diane Nocito, Varunseelan Murugaiyan, Jauhar Ali, Ambika Pandey, Carlos Casal, Jr., Erik Jon De Asis and Niña Gracel Dimaano

Biology 2025, 14(4), 413; https://doi.org/10.3390/biology14040413 - 13 Apr 2025

Viewed by 1126

Abstract

The direct-seeded rice (DSR) system is poised to become the dominant rice cultivation method due to its advantages, including reduced water usage, less labor requirements, decreased greenhouse gas emissions, and improved adaptation to climate change. However, weeds, particularly jungle rice (Echinochloa colona), significantly hinder DSR and cause substantial yield losses. This study aimed to develop rice cultivars competitive against jungle rice through selective breeding, focusing on early seed germination (ESG) and seedling vigor (ESV). We utilized 181 early-backcross selective introgression breeding lines (EB-SILs) developed using Green Super Rice (GSR) technology by backcrossing Weed Tolerant Rice1 (WTR1) with three donor parents, Haoannong, Cheng Hui 448, and Y134. Using the tunable genotyping-by-sequencing (tGBS^®, Data2Bio Technologies, Ames, IA, USA) method, we identified 3971 common single nucleotide polymorphisms (SNPs) that facilitated the mapping of 19 novel quantitative trait loci (QTLs) associated with weed competitiveness—eight linked to ESG traits and eleven to ESV traits. Notably, all QTLs were novel except qRPH1, linked to relative plant height at 14 and 21 days after sowing. Key QTLs were located on chromosomes 2, 3, 5, 6, 8, 9, 10, and 12. Candidate genes identified within these QTLs are implicated in the plant’s response to various abiotic and biotic stresses. Our findings enhance the understanding of the genetic basis for ESG and ESV traits critical for weed competitiveness, supporting marker-assisted and genomic selection approaches for breeding improved rice varieties. Furthermore, this research lays the groundwork for employing gene expression, cloning, and CRISPR editing strategies to combat jungle rice, with potential applications for other weed species and contributing to effective integrated weed management in the DSR system. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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19 pages, 7217 KiB

Open AccessArticle

Isolation of OsMetAP10, a Peptidase_M24 Superfamily Gene, Regulating Heading Date in Rice

by Quanyi Sun, Jianhua Zhao, Guangda Wang, Yu Wang, Yuntao Zhu, Yu Yan, Zihang Chen, Zongxiang Chen, Zhiming Feng and Shimin Zuo

Biology 2025, 14(2), 178; https://doi.org/10.3390/biology14020178 - 10 Feb 2025

Cited by 1 | Viewed by 594

Abstract

The heading date is one of the important traits in rice, which greatly affects grain yield and regional adaptability. Although the flowering pathways in rice have been extensively investigated, the genes involved in flowering remain largely unknown. Here, we report a rice lhd mutant, which showed late flowering under both long-day (LD) and short-day (SD) conditions. Through MutMap+ and linkage analysis, a deletion mutation in OsMetAP10 was inferred as the most likely candidate for lhd late flowering. OsMetAP10 encodes a methionine aminopeptidase that belongs to the peptidase_M24 subfamily III. The OsMetAP10 gene is constitutively expressed in rice and is induced by light, with a rhythmic expression pattern. OsMetAP10 knockout lines displayed late heading as the lhd mutation, while no alternations in morphology and heading were observed on OsMetAP10 overexpression lines, further confirming the mutation of OsMetAP10 as responsible for the late heading of lhd. Through RT-qPCR and transcriptome analysis, we revealed that the upregulated expression of the FT-like gene OsFLT4, a negatively flowering regulator, and the downregulation of flower development-related genes, OsMADS14, OsMADS15, and OsMADS34, played critical roles in determining the late flowering of the OsMetAP10 mutation. This study reports a new gene affecting flowering and provides a new insight into the role of OsMetAP10 in regulating rice heading. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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17 pages, 2094 KiB

Open AccessArticle

Identification of Candidate Genes for Cold Tolerance at Seedling Stage by GWAS in Rice (Oryza sativa L.)

by Huimin Shi, Wenyu Zhang, Huimin Cao, Laiyuan Zhai, Qingxin Song and Jianlong Xu

Biology 2024, 13(10), 784; https://doi.org/10.3390/biology13100784 - 30 Sep 2024

Viewed by 1340

Abstract

Due to global climate change, cold temperatures have significantly impacted rice production, resulting in reduced yield and quality. In this study, we investigated two traits related to the cold tolerance (CT) of 1992 diverse rice accessions at the seedling stage. Geng accessions exhibited higher levels of CT compared to xian accessions, with the GJ-tmp subgroup displaying the strongest CT. However, extreme CT accessions were also identified within the xian subspecies. Through GWAS analysis based on the survival rate (SR) and leaf score of cold tolerance (SCT), a total of 29 QTLs associated with CT at the seedling stage were identified, among which four QTLs (qSR3.1a, qSR4.1a, qSR11.1x, and qSR12.1a) were found to be important. Furthermore, five candidate genes (LOC_Os03g44760, LOC_Os04g06900, LOC_Os04g07260, LOC_Os11g40610, and LOC_Os12g10710) along with their favorable haplotypes were identified through gene function annotation and haplotype analysis. Pyramiding multiple favorable haplotypes resulted in a significant improvement in CT performance. Subsequently, three selected accessions (CX534, B236, and IRIS_313-8565), carrying different superior alleles for CT, were selected and recommended for molecular breeding for CT using marker-assisted selection (MAS). The findings from this study provide valuable resources for enhancing rice’s ability for CT while laying a foundation for the future cloning of novel genes involved in conferring CT. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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10 pages, 1535 KiB

Open AccessEditor’s ChoiceArticle

Generation of Two-Line Restorer Line with Low Chalkiness Using Knockout of Chalk5 through CRISPR/Cas9 Editing

by Gucheng Fan, Jiefeng Jiang, Yu Long, Run Wang, Famao Liang, Haiyang Liu, Junying Xu, Xianjin Qiu and Zhixin Li

Biology 2024, 13(8), 617; https://doi.org/10.3390/biology13080617 - 15 Aug 2024

Cited by 1 | Viewed by 1330

Abstract

Chalkiness is an important grain quality trait in rice. Chalk5, encoding a vacuolar H⁺-translocating pyrophosphatase, is a major gene affecting both the percentage of grains with chalkiness (PGWC) and chalkiness degree (DEC) in rice. Reducing its expression can decrease both PGEC and DEC. In this study, the first exon of Chalk5 was edited in the elite restorer line 9311 using the CRISPR/Cas9 system and two knockout mutants were obtained, one of which did not contain the exogenous Cas9 cassette. PGWC and DEC were both significantly reduced in both mutants, while the seed setting ratio (SSR) was also significantly decreased. Staggered sowing experiments showed that the chalkiness of the mutants was insensitive to temperature during the grain-filling stage, and the head milled rice rate (HMRR) could be improved even under high-temperature conditions. Finally, in the hybrid background, the mutants showed significantly reduced PGWC and DEC without changes in other agronomic traits. The results provide important germplasm and allele resources for breeding high-yield rice varieties with superior quality, especially for high-yield indica hybrid rice varieties with superior quality in high-temperature conditions. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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13 pages, 11033 KiB

Open AccessArticle

The Rice YL4 Gene Encoding a Ribosome Maturation Domain Protein Is Essential for Chloroplast Development

by Yunguang Sun, Yanxia Liu, Youze Zhang, Dongzhi Lin, Xiaobiao Pan and Yanjun Dong

Biology 2024, 13(8), 580; https://doi.org/10.3390/biology13080580 - 31 Jul 2024

Viewed by 1219

Abstract

Chloroplast RNA splicing and ribosome maturation (CRM) domain proteins are a family of plant-specific proteins associated with RNA binding. In this study, we have conducted a detailed characterization of a novel rice CRM gene (LOC_Os04g39060) mutant, yl4, which showed yellow-green leaves at all the stages, had fewer tillers, and had a decreased plant height. Map-based cloning and CRISPR/Cas9 editing techniques all showed that YL4 encoded a CRM domain protein in rice. In addition, subcellular localization revealed that YL4 was in chloroplasts. YL4 transcripts were highly expressed in all leaves and undetectable in roots and stems, and the mutation of YL4 affected the transcription of chloroplast-development-related genes. This study indicated that YL4 is essential for chloroplast development and affects some agronomic traits. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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15 pages, 4187 KiB

Open AccessArticle

Genetic Analysis and Fine Mapping of QTL for the Erect Leaf in Mutant mths29 Induced through Fast Neutron in Wheat

by Zhixin Yang, Jiayu Gu, Minghui Zhao, Xiaofeng Fan, Huijun Guo, Yongdun Xie, Jinfeng Zhang, Hongchun Xiong, Linshu Zhao, Shirong Zhao, Yuping Ding, Fuquan Kong, Li Sui, Le Xu and Luxiang Liu

Biology 2024, 13(6), 430; https://doi.org/10.3390/biology13060430 - 11 Jun 2024

Viewed by 1329

Abstract

The erect leaf plays a crucial role in determining plant architecture, with its growth and development regulated by genetic factors. However, there has been a lack of comprehensive studies on the regulatory mechanisms governing wheat lamina joint development, thus failing to meet current breeding demands. In this study, a wheat erect leaf mutant, mths29, induced via fast neutron mutagenesis, was utilized for QTL fine mapping and investigation of lamina joint development. Genetic analysis of segregating populations derived from mths29 and Jimai22 revealed that the erect leaf trait was controlled by a dominant single gene. Using BSR sequencing and map-based cloning techniques, the QTL responsible for the erect leaf trait was mapped to a 1.03 Mb physical region on chromosome 5A. Transcriptome analysis highlighted differential expression of genes associated with cell division and proliferation, as well as several crucial transcription factors and kinases implicated in lamina joint development, particularly in the boundary cells of the preligule zone in mths29. These findings establish a solid foundation for understanding lamina joint development and hold promise for potential improvements in wheat plant architecture. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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Review

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16 pages, 1466 KiB

Open AccessReview

African Cultivated, Wild and Weedy Rice (Oryza spp.): Anticipating Further Genomic Studies

by Babatunde O. Kehinde, Lingjuan Xie, Beng-Kah Song, Xiaoming Zheng and Longjiang Fan

Biology 2024, 13(9), 697; https://doi.org/10.3390/biology13090697 - 5 Sep 2024

Cited by 1 | Viewed by 1765

Abstract

Rice is a staple crop in sub-Saharan Africa, and it is mostly produced by Asian cultivars of Oryza sativa that were introduced to the continent around the fifteenth or sixteenth century. O. glaberrima, the native African rice, has also been planted due to its valuable traits of insect and drought tolerance. Due to competition and resistance evolution, weedy rice has evolved from O. sativa and O. glaberrima, posing an increasing threat to rice production. This paper provides an overview of current knowledge on the introduction and domestication history of cultivated rice in Africa, as well as the genetic properties of African weedy rice that invades paddy fields. Recent developments in genome sequencing have made it possible to uncover findings about O. glaberrima’s population structure, stress resilience genes, and domestication bottleneck. Future rice genomic research in Africa should prioritize producing more high-quality reference genomes, quantifying the impact of crop–wild hybridization, elucidating weed adaptation mechanisms through resequencing, and establishing a connection between genomic variation and stress tolerance phenotypes to accelerate breeding efforts. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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22 pages, 2617 KiB

Open AccessReview

Molecular Basis of Plant–Pathogen Interactions in the Agricultural Context

by Usman Ijaz, Chenchen Zhao, Sergey Shabala and Meixue Zhou

Biology 2024, 13(6), 421; https://doi.org/10.3390/biology13060421 - 6 Jun 2024

Cited by 1 | Viewed by 3981

Abstract

Biotic stressors pose significant threats to crop yield, jeopardizing food security and resulting in losses of over USD 220 billion per year by the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements to plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have offered new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel avenues for disrupting the molecular compatibility of pathogens and for introducing durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R-gene-based plant genome-engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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