Location: Crop Genetics Research
2025 Annual Report
Objectives
1. Characterize the genetic mechanisms for controlling nematode resistance for diploid cotton species.
1.A. Genetic characterization of reniform nematode resistance for selected G. arboreum germplasm accessions.
2. Transfer novel nematode resistance identified for diploid cotton species to tetraploid upland cotton.
2.A. Introgression of reniform nematode resistance from G. arboreum germplasm accessions into upland cotton cultivars.
3. Determine environmental influences on nematode infection, development, and reproduction on cotton lines.
3.A. Determine soil temperature effects on nematode infection, development, and reproduction on cotton lines.
3.B. Determine soil moisture effects on nematode infection, development, and reproduction on cotton lines.
Approach
Develop populations by crossing resistant accessions with one or more Gossypium (G.) arboreum accessions classified as susceptible or highly susceptible to determine the inheritance of the resistance. Ovule culture will be used to introgress resistance from G. arboreum accessions into G. hirsutum varieties. Gossypium accessions with high levels of resistance to reniform nematode will be evaluated in growth chamber experiments to measure the effects of soil temperature and soil moisture stress on the number of infections, rate of development of females after infection, and production of eggs.
Progress Report
Reniform nematode (Rotylenchulus reniformis) is a yield-limiting factor for US cotton production. The estimated yield loss caused by this microscopic parasitic worm was 40.2 thousand metric tons in 2024, which is 1.28% of the total US cotton production, and represents a loss of USD $60 M. In several southeast states, such as Alabama, Louisiana, and Mississippi, this parasite causes more dramatic yield losses.
Widely used chemical nematicides only provide protection for cotton seedlings and nematode populations can dramatically rebound during the growing season of cotton. Crop rotation can reduce the nematode population, but long rotational cycles are required to significantly reduce the population enough to have an economic benefit. Therefore, it is not a preferred way to manage this parasite. Growing resistant cotton cultivars would be the most economical and effective approach for reniform nematode management and developing upland cotton cultivars with resistance to reniform nematode is a common goal for cotton breeding programs. However, high-level resistance to reniform nematode was not found in widely cultivated upland cotton (G. hirsutum), but was identified in some other species, such as G. arboreum. The goals of this research include identifying G. arboreum resistance sources, understanding the genetic mechanism of resistance, transferring resistance from G. arboreum into G. hirsutum, and investigating the impact of soil temperature/moisture on reniform nematode persistence and damage. To achieve these goals, various approaches were applied in our research and progress during FY 2025 is summarized below.
Objective 1 focused on developing segregating populations for studying the genetic mechanism of resistance from G. arboreum to reniform nematode. Seven resistant G. arboreum germplasm accessions (A2-190, A2-272, A2-354, A2-514, A2-690, A2-737, A2-995) and three susceptible accessions (A2-20, A2-40, A2-101) were used to make various crosses, including Resistant x Resistant, Resistant x Susceptible and Susceptible x Susceptible types of crosses in 2024.The F1 seed of these crosses was planted in the field, greenhouse, or at the Cotton Winter Nursery (Costa Rica) for producing F2 seed. The F2 generations of these crosses will be evaluated for resistance/susceptibility to reniform nematode. Seed from 261 individual F2 plants from the cross A2- 711(resistant, R) x A2-101 (susceptible, S) were planted as F2:3 progeny rows in the field in 2024. Leaf tissues were collected for DNA extraction. These F2:3 lines are being tested for resistance to reniform nematode and genotyped using the genotyping–by–sequencing approach. The phenotypic and genotypic data will be analyzed to map quantitative trait loci (QTL) controlling resistance to reniform nematode.
Another study for mapping QTL controlling resistance to reniform nematode was carried out with G. arboreum resistant accessions A2-87 (PI 417895) and A2-113 (PI 529740) which were crossed with susceptible accession A2-101 (PI 529729) to develop F2 populations. The 174 and 172 individual plants of these two F2 populations were tested for resistance to reniform nematode and genotyped using genotyping-by-sequencing (GBS) approach. In the (A2-101 x A2-87) F2 population, QTLs were found on chromosomes 10 and 12. Twenty-five plant disease resistance genes and three Meloidogyne-induced cotton (MIC) genes associated with nematode attack response were found within the QTL region on chromosome 10; eight receptor-like protein EIX genes were found in the QTL region on chromosome 12, which could act as pattern recognition receptors (PRR) involved in plant defense against fungal pathogens, the genes controlling resistance to reniform nematode need to further identified. These results were presented at 2024 ASA- CSSA-SSSA annual meeting, and a manuscript is in preparation. In the (A2- 113 x A2-101) F2 population, QTLs were mapped on chromosomes 1, 5, and 13. Plant disease resistance genes and other genes involved in resistance to nematodes were found. These results were presented at 2025 Beltwide Cotton Conferences, and a manuscript is in preparation. More studies are underway to understand why there were not QTLs in common between the populations.
Objective 2 focused on the development of synthetic tetraploid and hexaploid bridging lines. The Gossypium genus consists of seven tetraploid species (52 chromosomes, species genome symbols AD1 to AD7) and 48 diploid species (26 chromosomes, species genome symbols A to G and K). Upland cotton (AD1) and Pima cotton (AD2) account for approximately 97% and 3% of the US cotton production. Diploid species contain many desirable genes, such as resistance to reniform nematode, which can be used for genetic improvement of upland cotton. However, crossing tetraploids with diploids often results in embryo abortion, and the derived triploid plants would be sterile. To introduce useful genes from diploid Gossypium species into tetraploid upland cotton, chromosome doubling through colchicine treatment was used to produce synthetic tetraploid and hexaploid bridging lines. In summary, upland cultivars were crossed with several diploid species. Triploid plants were obtained by tissue culture of ovules 3 days after pollination. A few triploid seeds were also harvested directly from cotton plants. Three hexaploid plants, 2(DP90 x D5-4), 2(SG747 x A2-354), and 2(MD10-5 x A2-354), were obtained after colchicine treatment to double the chromosome number. These hexaploid lines were crossed with diploid plants and produced fertile tetraploid seeds.
Diploid G. arboreum accessions A2-190, A2-272, A2-354, A2-514, A2-690, and A2-737 are resistant to reniform nematode. Seedlings of 5 crosses (A2-690 x A2-190). (A2-690 x A2-272), (A2-737 x A2-190), (A2-737 x A2-354), and (A2-737 x A2-514) were treated with colchicine to double the chromosome number and generate synthetic tetraploid plants. These synthetic tetraploid plants were crossed with upland cotton or Pima cotton cultivars and produced seeds. The resulting seeds will be further evaluated, including tetraploid lines with diploid genes for resistance to reniform nematode.
To introduce reniform nematode resistance from diploid species into upland cotton, the hexaploid lines were crossed with diploid species, and the synthetic tetraploid plants were crossed with upland cotton and Pima cotton cultivars. Four resulting tetraploid F1 hybrids were propagated in the greenhouse or the Cotton Winter Nursery to produce F2 seeds. So far, 22 F1 lines and one F2 population have been planted in a growth chamber for screening with reniform nematodes.
Objective 3 involved investigating the impact of soil temperature on reniform nematode infection, development and reproduction. Two resistant Pima cotton lines GB713 and TX 110 and a susceptible control upland cotton cultivar Deltapine 16 were included in the tests. A soil temperature at 28 C is considered favorable for reniform nematodes while 32 C is too warm. Two tests each at 24 C and 28 C have been finished. The last two tests at 32 C will be conducted in July and August 2025. Then the test results at the three temperatures (24 C, 28 C and 32 C) will be analyzed. The results will be made available through a conference presentation and published.
Accomplishments
1. Development of tetraploid Gossypium arboreum and hexaploid lines for exploitation of diploid cotton.. Diploid cotton species have many desirable traits that the cultivated tetraploid upland cotton does not have. However, crossing diploid species with tetraploid cotton to obtain hybrid seeds is rarely successful, impeding the use of these important germplasm resources. ARS researchers at Stoneville, Mississippi have developed five synthetic tetraploid G. arboreum and three interspecific hexaploid lines through a technique to double chromosome number. These derived tetraploid G. arboreum plants can be directly crossed with upland or Pima cotton and produce fertile seed. The hexaploid lines can be crossed with diploid germplasm to produce hybrid tetraploid seeds. These tetraploid G. arboreum plants and interspecific hexaploid lines can be used by cotton breeders to directly transfer useful traits from diploid to tetraploid cotton without the need for in vitro techniques or chemical chromosome doubling. These lines are currently being used to transfer reniform nematode resistance to cotton that can be grown by US farmers (A book chapter is in press). As root feeding reniform nematode parasites routinely cause millions of dollars in damage to commercial cotton in the US.